Mendel and Darwin.

Evolution by natural selection is an explicitly genetic theory. Darwin recognized that a working theory of inheritance was central to his theory and spent much of his scientific life seeking one. The seeds of his attempt to fill this gap, his "provisional hypothesis" of pangenesis, appear in his notebooks when he was first formulating his evolutionary ideas. Darwin, in short, desperately needed Mendel. In this paper, we set Mendel's work in the context of experimental biology and animal/plant breeding of the period and review both the well-known story of possible contact between Mendel and Darwin and the actual contact between their ideas after their deaths. Mendel's contributions to evolutionary biology were fortuitous. Regardless, it is Mendel's work that completed Darwin's theory. The modern theory based on the marriage between Mendel's and Darwin's ideas as forged most comprehensively by R. A. Fisher is both Darwin's achievement and Mendel's.

Speciation by physiological selection of environmentally acquired traits.

A chance mutation affecting a single or extremely few individuals in a continuous population will be quickly diluted through interbreeding. Charles Darwin fully appreciated this difficulty with relying on natural selection alone, and suggested an enabling role for geographical isolation in the origin of species. However, Darwin also believed in evolution by the inheritance of acquired traits and in populations of interbreeding animals, both of which would need a different isolating mechanism to overcome dilution and play a role in animal evolution. Historically disputed, the inheritance of acquired characters is now increasingly accepted as a phenomenon, and Charles Darwin himself is acknowledged as closely pre-empting the type of physiology necessary to mediate it in his hypothesis of 'pangenesis'. In this article, we question how the inheritance of acquired traits might overcome the problem of dilution by interbreeding and contribute to evolution. Specifically, we describe how Darwin's young protégé, George Romanes, developed ideas he discussed with Darwin and extended pangenesis to include a conceivable solution published after Darwin's death: physiological selection of fertility. In light of the 'rediscovery' of pangenesis, here we recount physiological selection as a testable hypothesis to explain how environmentally acquired characteristics could become coupled to the generation of species.

Evolutionary feedback from the environment shapes mechanisms that generate genome variation.

Darwin recognized that 'a grand and almost untrodden field of inquiry will be opened, on the causes and laws of variation.' However, because the Modern Synthesis assumes that the intrinsic probability of any individual mutation is unrelated to that mutation's potential adaptive value, attention has been focused on selection rather than on the intrinsic generation of variation. Yet many examples illustrate that the term 'random' mutation, as widely understood, is inaccurate. The probabilities of distinct classes of variation are neither evenly distributed across a genome nor invariant over time, nor unrelated to their potential adaptive value. Because selection acts upon variation, multiple biochemical mechanisms can and have evolved that increase the relative probability of adaptive mutations. In effect, the generation of heritable variation is in a feedback loop with selection, such that those mechanisms that tend to generate variants that survive recurring challenges in the environment would be captured by this survival and thus inherited and accumulated within lineages of genomes. Moreover, because genome variation is affected by a wide range of biochemical processes, genome variation can be regulated. Biochemical mechanisms that sense stress, from lack of nutrients to DNA damage, can increase the probability of specific classes of variation. A deeper understanding of evolution involves attention to the evolution of, and environmental influences upon, the intrinsic variation generated in gametes, in other words upon the biochemical mechanisms that generate variation across generations. These concepts have profound implications for the types of questions that can and should be asked, as omics databases become more comprehensive, detection methods more sensitive, and computation and experimental analyses even more high throughput and thus capable of revealing the intrinsic generation of variation in individual gametes. These concepts also have profound implications for evolutionary theory, which, upon reflection it will be argued, predicts that selection would increase the probability of generating adaptive mutations, in other words, predicts that the ability to evolve itself evolves.

Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies.

Human activity changes multiple factors in the environment, which can have positive or negative synergistic effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwin's finches in the Galápagos Islands. We experimentally manipulated nest fly abundance in urban and non-urban locations and then characterized nestling health, fledging success, diet, and gene expression patterns related to host defense. Fledging success of non-parasitized nestlings from urban (79%) and non-urban (75%) nests did not differ significantly. However, parasitized, non-urban nestlings lost more blood, and fewer nestlings survived (8%) compared to urban nestlings (50%). Stable isotopic values (δ15 N) from urban nestling feces were higher than those from non-urban nestlings, suggesting that urban nestlings are consuming more protein. δ15 N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized, urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro-inflammatory response (innate immunological resistance), compared to parasitized, non-urban nestlings. In contrast, parasitized non-urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro-inflammatory responses to resist parasites but also recovering more blood cells to tolerate blood loss. Although non-urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.

Geometry and dynamics link form, function, and evolution of finch beaks.

Darwin's finches are a classic example of adaptive radiation, exemplified by their adaptive and functional beak morphologies. To quantify their form, we carry out a morphometric analysis of the three-dimensional beak shapes of all of Darwin's finches and find that they can be fit by a transverse parabolic shape with a curvature that increases linearly from the base toward the tip of the beak. The morphological variation of beak orientation, aspect ratios, and curvatures allows us to quantify beak function in terms of the elementary theory of machines, consistent with the dietary variations across finches. Finally, to explain the origin of the evolutionary morphometry and the developmental morphogenesis of the finch beak, we propose an experimentally motivated growth law at the cellular level that simplifies to a variant of curvature-driven flow at the tissue level and captures the range of observed beak shapes in terms of a simple morphospace. Altogether, our study illuminates how a minimal combination of geometry and dynamics allows for functional form to develop and evolve.

Morphological ghosts of introgression in Darwin's finch populations.

Many species of plants, animals, and microorganisms exchange genes well after the point of evolutionary divergence at which taxonomists recognize them as species. Genomes contain signatures of past gene exchange and, in some cases, they reveal a legacy of lineages that no longer exist. But genomic data are not available for many organisms, and particularly problematic for reconstructing and interpreting evolutionary history are communities that have been depleted by extinctions. For these, morphology may substitute for genes, as exemplified by the history of Darwin's finches on the Galápagos islands of Floreana and San Cristóbal. Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris in 1835. The populations became extinct in the next few decades, partly due to destruction of Opuntia cactus by introduced goats, whereas Geospiza fortis has persisted to the present. We used measurements of large samples of G. fortis collected for museums in the period 1891 to 1906 to test for unusually large variances and skewed distributions of beak and body size resulting from introgression. We found strong evidence of hybridization on Floreana but not on San Cristóbal. The skew is in the direction of the absent G. magnirostris We estimate introgression influenced 6% of the frequency distribution that was eroded by selection after G. magnirostris became extinct on these islands. The genetic residuum of an extinct species in an extant one has implications for its future evolution, as well as for a conservation program of reintroductions in extinction-depleted communities.

Invasion on So Grand a Scale: Darwin, Lyell, and Invasive Species.

The importance of naturalization-the establishment of species introduced into foreign places-to the early development of Darwin's theory of evolution deserves historical attention. Introduced and invasive European species presented Darwin with interpretive challenges during his service as naturalist on the HMS Beagle. Species naturalization and invasive species strained the geologist Charles Lyell's creationist view of the organic world, a view which Darwin adopted during the voyage of the Beagle but came to question afterward. I suggest that these phenomena primed Darwin to question the "stability of species." I then examine the role of introduced and invasive species in Darwin's early theorizing and negotiation with Lyell's ideas, recorded in his post-voyage "transmutation notebooks." Therein, the subject was an inflection point in his contention with Lyell's views and moreover, his theorizing on invasive species occasioned some of his earliest inklings of natural selection. Finally, I examine how naturalization was crucial to Lyell's own eventual conversion to evolutionism. I conclude with brief reflections on the implications of this narrative for our understanding of Darwin's reasoning, his intellectual relationship to Lyell, and the historical context that shaped his theory.

Darwin and the White Shipwrecked Sailor: Beyond Blending Inheritance and the Jenkin Myth.

This paper revisits Fleeming Jenkin's anonymous review of Charles Darwin's Origin of Species, published in the North British Review in June 1867. This review is usually revered for its impact on Darwin's theory of descent with modification. Its classical interpretation states that Jenkin, a Professor of Engineering at the University of Edinburgh, made a compelling case against natural selection based on the fact of "blending inheritance" and the "swamping" of advantageous variations. Those themes, however, are strikingly absent from Jenkin's text. They were later read into Jenkin's text by scholars trying to explain how Darwinian selection was reconciled with Mendelian genes and the birth of the Modern Synthesis. While many scholars have tried to measure Jenkin's effect on Darwin, the value of the 1867 review remains unclear. This paper re-examines its content and concludes that Jenkin's "able review" was in fact written by an engineer whose competencies in biology were very low. Focusing on the figure of the shipwrecked white sailor isolated on an island inhabited by Black people, this paper also underlines the racial assumptions behind Jenkin's review. "Blending inheritance" is thus a theme linked to theoretical reworkings on the question of race and skin colors, taking its root in Galton's typology of heredity. Darwin was probably mostly unimpressed by Jenkin's review. The problems raised by the review were not so much "blending inheritance" and "swamping" but a conundrum of problems related to the effects of intercrossing on variation and reversion.

It Ain't Necessarily So: Ludwig Boltzmann's Darwinian Notion of Entropy.

Ludwig Boltzmann's move in his seminal paper of 1877, introducing a statistical understanding of entropy, was a watershed moment in the history of physics. The work not only introduced quantization and provided a new understanding of entropy, it challenged the understanding of what a law of nature could be. Traditionally, nomological necessity, that is, specifying the way in which a system must develop, was considered an essential element of proposed physical laws. Yet, here was a new understanding of the Second Law of Thermodynamics that no longer possessed this property. While it was a new direction in physics, in other important scientific discourses of that time-specifically Huttonian geology and Darwinian evolution, similar approaches were taken in which a system's development followed principles, but did so in a way that both provided a direction of time and allowed for non-deterministic, though rule-based, time evolution. Boltzmann referred to both of these theories, especially the work of Darwin, frequently. The possibility that Darwin influenced Boltzmann's thought in physics can be seen as being supported by Boltzmann's later writings.

ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.

BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.

Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication.

'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.

Beak morphometry and morphogenesis across avian radiations.

Adaptive avian radiations associated with the diversification of bird beaks into a multitude of forms enabling different functions are exemplified by Darwin's finches and Hawaiian honeycreepers. To elucidate the nature of these radiations, we quantified beak shape and skull shape using a variety of geometric measures that allowed us to collapse the variability of beak shape into a minimal set of geometric parameters. Furthermore, we find that just two measures of beak shape-the ratio of the width to length and the normalized sharpening rate (increase in the transverse beak curvature near the tip relative to that at the base of the beak)-are strongly correlated with diet. Finally, by considering how transverse sections to the beak centreline evolve with distance from the tip, we show that a simple geometry-driven growth law termed 'modified mean curvature flow' captures the beak shapes of Darwin's finches and Hawaiian honeycreepers. A surprising consequence of the simple growth law is that beak shapes that are not allowed based on the developmental programme of the beak are also not observed in nature, suggesting a link between evolutionary morphology and development in terms of growth-driven developmental constraints.

Towards understanding insect species introduction and establishment: A community-level barcoding approach using island beetles.

Since Darwin put forward his opposing hypotheses to explain the successful establishment of species in areas outside their native ranges, the preadaptation and competition-relatedness hypotheses, known as Darwin's naturalization conundrum, numerous studies have sought to understand the relative importance of each. Here, we take advantage of well-characterized beetle communities across laurel forests of the Canary Islands for a first evaluation of the relative support for Darwin's two hypotheses within arthropods. We generated a mitogenome backbone tree comprising nearly half of the beetle genera recorded within the Canary Islands for the phylogenetic placement of native and introduced species sampled in laurel forests, using cytochrome c oxidase I (COI) sequences. For comparative purposes, we also assembled and phylogenetically placed a data set of COI sequences for introduced beetle species that were not sampled within laurel forests. Our results suggest a stronger effect of species preadaptation over resource competition, while also revealing an underappreciated shortfall in arthropod biodiversity data-knowledge of species as being native or introduced. We name this the Humboldtean shortfall and suggest that similar studies using arthropods should incorporate DNA barcode sequencing to mitigate this problem.

Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.).

When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and F. diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀ × H♂). To determine why F. heteroclitus × F. diaphanus F1 hybrids (H♀ × D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference and male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, whereas F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀ × D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀ × H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀ × H♂ crosses had a higher hatching success than F. diaphanus crosses at 10 ppt, which may further increase their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.

Darwin's naturalization conundrum can be explained by spatial scale.

Darwin proposed two seemingly contradictory hypotheses regarding factors influencing the outcome of biological invasions. He initially posited that nonnative species closely related to native species would be more likely to successfully establish, because they might share adaptations to the local environment (preadaptation hypothesis). However, based on observations that the majority of naturalized plant species in the United States belonged to nonnative genera, he concluded that the lack of competitive exclusion would facilitate the establishment of alien invaders phylogenetically distinct from the native flora (competition-relatedness hypothesis). To date, no consensus has been reached regarding these opposing hypotheses. Here, following Darwin, we use the flora of the United States to examine patterns of taxonomic and phylogenetic relatedness between native and nonnative taxa across thousands of nested locations ranging in size and extent, from local to regional scales. We find that the probability of observing the signature of environmental filtering over that of competition increases with spatial scale. Further, native and nonnative species tended to be less related in warm, humid environments. Our work provides an empirical assessment of the role of observation scale and climate in biological invasions and demonstrates that Darwin's two opposing hypotheses need not be mutually exclusive.

Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots.

Angraecum, commonly known as Darwin's orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine-cytosine (GC) content of 36.6-36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnSGCU-trnGGCC, ycf1-trnNGGU, trnNGUU-rpl32, psaC-ndhE and trnSGCU-trnGGCC) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum.

A "Mean Quarrelsome Spirit:" Controversy in British Systematics, 1822-1836.

British systematics was distinctly marked by a raft of vituperative controversies around the turn of the 1830s. After the local collapse of broad consensus in the Linnaean system by 1820, the emergence of new schemes of classification-most notably, the "quinarian" system of William Sharp Macleay-brought with it an unprecedented register of public debate among zoologists in Britain, one which a young Charles Darwin would bitterly describe to his friend John Stevens Henslow in October 1836 as possessing a "mean quarrelsome spirit," conducted in "a manner anything but like that of gentlemen." This article aims to provide a social and conceptual account of the remarkable tenor of zoological discourse in Britain in the late 1820s and early 1830s, with joint attention to the philosophical and interpersonal commitments at play. In doing so, it analyzes the three of the period's most striking public controversies, each of which counted key advocates of the quinarian system as central participants.

Claude Bernard's non reception of Darwinism.

The aim of this paper is to explain why, while Charles Darwin was well recognized as a scientific leader of his time, Claude Bernard never really regarded Darwinism as a scientific theory. The lukewarm reception of Darwin at the Académie des Sciences of Paris and his nomination to a chair only after 8 years contrasts with his prominence, and Bernard's attitude towards Darwin's theory of species evolution belongs to this French context. Yet we argue that Bernard rejects the scientific value of Darwinian principles mainly for epistemological reasons. Like Darwin, Bernard was interested in hereditary processes, and planned to conduct experiments on these processes that could lead to species transformation. But the potential creation of new forms of life would not vindicate Darwinism since biologists can only explain the origin of morphotypes and morphological laws by the means of untestable analogies. Because it can be the object neither of experiments nor of any empirical observation, phylogeny remains out of science's scope. Around 1878 Bernard foresaw a new general physiology based on the study of protoplasm, which he saw as the agent of all basic living phenomena. We will analyze why Bernard regarded Darwinism as part of metaphysics, yet still referred to Darwinians in his latter works in 1878. Basically, the absence of a scientific reception of Darwinism in Bernard's work should not obscure its philosophical reception, which highlights the main principles of Bernard's epistemology.

Darwin's dark matter: utter extinction.

Species that died without leaving descendants Darwin called 'utterly extinct'. They far outnumber the ancestors of all living things, so they resemble the dark matter of modern cosmology, which far outweighs visible matter. He realized in 1837 that their absence is what creates the groups in a natural classification. In his Notebook B he combined the idea that species multiply with the idea that ancestors' relatives must mostly be extinct. The fossil Megatherium was utterly extinct. The iconic branching 'I think' diagram shows extinction causing the origin of genera by eliminating intermediate species. Darwin's concept of taxonomic ranks, starting with the genus, was informed by his interaction with taxonomists. Based on his familiarity with demography, Darwin reasoned that the survival of transitional forms was unlikely, which helped him decide to focus at the species level. When drafting his theory in the 1840s, he left out these speculative ideas, but they emerged again in the 1850s when he realized his theory needed a cause for branches to diverge. His ecological answer worked at the species level, but his Principle of Divergence was unconvincing at higher taxonomic levels. In the Origin, Darwin repeatedly insisted on the importance of utter extinction.

From epigenotype to new genotypes: Relevance of epigenetic mechanisms in the emergence of genomic evolutionary novelty.

A fundamental question in evolutionary biology is how heritable variability originates. In Darwinian evolution a central focus was placed on the thinking that random variations are the material basis for the action of natural selection. Although randomness in Darwinian evolution can be interpreted from different angles, here I will focus on the assumption of equiprobability of mutations. I have reviewed the literature regarding epigenetic mechanisms causing biased genetic variability. Although it is interesting to find correlations between somatic epigenetic marks and evolution, causation between epigenetic changes and genomic evolutionary novelties can only be established when the epigenetic changes are interrogated in the germ line. Epigenetic changes are reported to influence the emergence of single nucleotide polymorphisms and copy number variations. On the other hand, epigenetic changes are known to be influenced by environmental exposures. This dual ability of epigenetic changes could mean that germ line epigenetically influenced mutations could have an important role in the emergence of genomic evolutionary novelties. The emergent knowledge on the relation of epigenetic changes and mutations will help to understand an underappreciated role of the environment in speciation and genomic divergence: that of influencer of genomic changes.