Network Theory and the Formation of Groups Without Evolutionary Forces

This paper presents a modified random network model to illustrate how groups can form in the absence of evolutionary forces, assuming groups are collections of entities at any level of organization. This model is inspired by the Zero Force Evolutionary Law, which states that there is always a tendency for diversity and complexity to increase in any evolutionary system containing variation and heredity. That is, in the absence of evolutionary forces, the expectation is a continual increase in diversity and complexity at any level of biological hierarchy. I show that, when modeled, this expectation of increasing variation results not only in the formation of groups, but also in a higher probability of group formation than is found in a model that is purely random.     

The influence of multiple functional demands on morphological diversification: A test on turtle shells

Organismal parts are often involved in the performance of more than one function. The role of trade‐offs in influencing phenotypic evolution of such parts is well‐studied; less well‐understood is their role in influencing phenotypic diversity. Increases in the number of functions a part is involved in may inhibit subsequent diversification, as the number of trade‐offs increases. Alternately, such an increase might promote phenotypic diversification, by increasing adaptive landscape complexity and promoting specialization for different roles. We compare these predictions by testing whether aquatic turtle shells, which resist loads, act as hydrodynamic elements, facilitate self‐righting, and exchange heat with the environment, differ in phenotypic diversity from those of terrestrial species, which perform all the same functions except for hydrodynamics. We used 53 3D landmarks digitized on 2722 specimens of 274 hard‐shelled turtle species to quantify shell shape variation, and a set of phylogenetic hypotheses to examine evolutionary patterns. Terrestrial turtles consistently had higher phenotypic diversity than aquatic species. Differences are not due to differences in the rates of evolution between the two groups, but rather differences in evolutionary mode. Thus this study supports the traditional view of the role of multiple functions in determining phenotypic diversity.     

Founder events predict changes in genetic diversity during human‐mediated range expansions

Intentional or accidental introduction of species to new locations is predicted to result in loss of genetic variation and increase the likelihood of inbreeding, thus reducing population viability and evolutionary potential. However, multiple introductions and large founder numbers can prevent loss of genetic diversity and may therefore facilitate establishment success and range expansion. Based on a meta‐analysis of 119 introductions of 85 species of plants and animals, we here show a quantitative effect of founding history on genetic diversity in introduced populations. Both introduction of large number of individuals and multiple introduction events significantly contribute to maintaining or even increasing genetic diversity in introduced populations. The most consistent loss of genetic diversity is seen in insects and mammals, whereas introduced plant populations tend to have higher genetic variation than native populations. However, loss or gain of genetic diversity does not explain variation in the extent to which plant or animal populations become invasive outside of their native range. These results provide strong support for predictions from population genetics theory with respect to patterns of genetic diversity in introduced populations, but suggest that invasiveness is not limited by genetic bottlenecks.     

Expansion of genome coding regions by acquisition of new genes

As it is the case for non-coding regions, the coding regions of organisms can be expanded or shrunk during evolutionary processes. However, the dynamics of coding regions are expected to be more correlated with functional complexity and diversity than are the dynamics of non-coding regions. Hence, it is interesting to investigate the increase of diversity in coding regions – the origin and evolution of new genes – because this provides a new component to the genetic variation underlying the diversity of living organisms. Here, we examine what is known about the mechanisms responsible for the increase in gene number. Every mechanism affects genomes in a distinct way and to a different extent and it appears that certain organisms favor particular mechanisms. The detail of some interesting gene acquisitions reveals the extreme dynamism of genomes. Finally, we discuss what is known about the fate of new genes and conclude that many of the acquisitions are likely to have been driven by natural selection; they increase functional complexity, diversity, and/or adaptation of species. Despite this, the correlation between complexity of life and gene number is low and closely related species (with very similar life histories) can have very different number of genes. We call this phenomenon the G-value paradox.     

Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae

Although discordance between taxonomic diversity and morphological disparity is common, little is known about the underlying dynamics that drive this decoupling. Early in the history of the Cambrian trilobite family Pterocephaliidae, there was an increase in taxonomic diversity and morphological diversity. As taxonomic diversity declined in the later history of the clade, range of variation stayed high and disparity continued to increase. However, per‐branch rates of morphological evolution estimated from a recent phylogeny decreased with time. Neither within‐trait nor within‐species variation increased or decreased, suggesting that the declining rates of morphological evolution were more likely related to ecological opportunity or niche partitioning, rather than increasing intrinsic constraints. This is further supported by evidence for increased biofacies associations throughout the time period. Thus, the high disparity seen at low taxonomic diversity late in the history of this clade was due to extinction – either random or targeting mean forms – rather than increased rates of morphological evolution. This pattern also provides a scenario that could account for instances of low taxonomic diversity but high morphological disparity in modern groups.     

Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems

Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta‐analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic‐like river systems. Simulations revealed that the three processes we considered (downstream‐biased dispersal, increase in habitat availability downstream and upstream‐directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream‐biased dispersal.     

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision‐making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = ?0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.     

SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS?

Evolutionary change in New World Monkey (NWM) skulls occurred primarily along the line of least resistance defined by size (including allometric) variation ( g_max ). Although the direction of evolution was aligned with this axis, it was not clear whether this macroevolutionary pattern results from the conservation of within population genetic covariance patterns (long‐term constraint) or long‐term selection along a size dimension, or whether both, constraints and selection, were inextricably involved. Furthermore, G ‐matrix stability can also be a consequence of selection, which implies that both, constraints embodied in g_max and evolutionary changes observed on the trait averages, would be influenced by selection. Here, we describe a combination of approaches that allows one to test whether any particular instance of size evolution is a correlated by‐product due to constraints ( g_max ) or is due to direct selection on size and apply it to NWM lineages as a case study. The approach is based on comparing the direction and amount of evolutionary change produced by two different simulated sets of net‐selection gradients ( β ), a size (isometric and allometric size) and a nonsize set. Using this approach it is possible to distinguish between the two hypotheses (indirect size evolution due to constraints or direct selection on size), because although both may produce an evolutionary response aligned with g_max , the amount of change produced by random selection operating through the variance/covariance patterns (constraints hypothesis) will be much smaller than that produced by selection on size (selection hypothesis). Furthermore, the alignment of simulated evolutionary changes with g_max when selection is not on size is not as tight as when selection is actually on size, allowing a statistical test of whether a particular observed case of evolution along the line of least resistance is the result of selection along it or not. Also, with matrix diagonalization (principal components [PC]) it is possible to calculate directly the net‐selection gradient on size alone (first PC [PC1]) by dividing the amount of phenotypic difference between any two populations by the amount of variation in PC1, which allows one to benchmark whether selection was on size or not.     

The formation of species pools: historical habitat abundance affects current local diversity

Aim Explanations of biogeographic diversity patterns have emphasized the role of large‐scale processes that determine species pools, whereas explanations of local patterns have not. We address the hypothesis that local diversity patterns are also primarily dependent on the size of the available species pools, which are expected to be large when the particular habitat type has been evolutionary more abundant, or in unproductive habitats due to shorter generation time and hence higher diversification rates. Location The Canary Islands. Methods We determined the geographic distribution and habitat requirements of all native vascular plant species in the Canary Islands. Species pools for each habitat type on particular islands were further split into two categories according to origin: either originating due to local diversification or due to natural immigration. The dependence of historical diversification and diversification rate on habitat type, area, age, altitude and distance to the mainland was tested with general linear mixed models weighed according to the Akaike information criterion. Results The largest portion of the local variation in plant species diversity was attributed to the historic (pre‐human) habitat area, although island age was also important. The diversification rate was higher in unproductive habitats of coastal scrub and summit vegetation. Main conclusion Our study supports the species pool hypothesis, demonstrating that natural local patterns of species diversity in different habitats mirror the abundance of those particular habitats in evolutionary history. It also supports the community‐level birth rate hypothesis, claiming that stressful conditions result in higher diversification rates. We conclude that much of the observed local variation in plant diversity can be attributed to the differing sizes of species pools evolved under particular habitat conditions, and that historic parameters are far more important determinants of local diversity than suggested by ecological theory.     

Gene duplication and divergence produce divergent MHC genotypes without disassortative mating

Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC‐disassortative mate choice. However, many species lack this expected pattern of MHC‐disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus‐specific primers for high‐throughput sequencing of two expressed MHC Class II B genes in Leach's storm‐petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene‐specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good statistical power, we consistently found random assortment of mates at MHC. Despite random mating, birds had MHC genotypes with functionally diverged alleles, averaging 13 amino acid differences in pairwise comparisons of exon 2 alleles within individuals. To test whether this high MHC diversity in individuals is driven by evolutionary divergence of the two duplicated genes, we built a phylogenetic permutation model. The model showed that genotypic diversity was strongly impacted by sequence divergence between the most common allele of each gene, with a smaller additional impact of monophyly of the two genes. Divergence of allele sequences between genes may have reduced the benefits of actively seeking MHC‐dissimilar mates, in which case the evolutionary history of duplicated genes is shaping the adaptive landscape of sexual selection.     

Social heterosis and the maintenance of genetic diversity at the genome level

Social heterosis is when individuals in groups or neighbourhoods receive a mutualistic benefit from across‐individual genetic diversity. Although it can be a viable evolutionary mechanism to maintain allelic diversity at a given locus, its efficacy at maintaining genome‐wide diversity is in question when multiple loci are being simultaneously selected. Therefore, we modelled social heterosis in a population of haploid genomes of two‐ or three‐linked loci. With such linkages, social heterosis decreases gametic diversity, but maintains allelic diversity. Genomes tend to survive as complimentary pairs, with alternate alleles at each locus (e.g. the pair AbC and aBc). The outcomes of selection appear similar to fitness epistasis but are novel in the sense that phenotypic interactions occur across rather than within individuals. The model’s results strongly suggest that strong linkage across gene loci actually increases the probability that social heterosis maintains significant genetic diversity at the level of the genome.     

A non‐invasive geometric morphometrics method for exploring variation in dorsal head shape in urodeles: sexual dimorphism and geographic variation in Salamandra salamandra

The study of morphological variation among and within taxa can shed light on the evolution of phenotypic diversification. In the case of urodeles, the dorso‐ventral view of the head captures most of the ontogenetic and evolutionary variation of the entire head, which is a structure with a high potential for being a target of selection due to its relevance in ecological and social functions. Here, we describe a non‐invasive procedure of geometric morphometrics for exploring morphological variation in the external dorso‐ventral view of urodeles' head. To explore the accuracy of the method and its potential for describing morphological patterns we applied it to two populations of Salamandra salamandra gallaica from NW Iberia. Using landmark‐based geometric morphometrics, we detected differences in head shape between populations and sexes, and an allometric relationship between shape and size. We also determined that not all differences in head shape are due to size variation, suggesting intrinsic shape differences across sexes and populations. These morphological patterns had not been previously explored in S. salamandra , despite the high levels of intraspecific diversity within this species. The methodological procedure presented here allows to detect shape variation at a very fine scale, and solves the drawbacks of using cranial samples, thus increasing the possibilities of using collection specimens and alive animals for exploring dorsal head shape variation and its evolutionary and ecological implications in urodeles. J. Morphol. 278:475–485, 2017. © 2017 Wiley Periodicals, Inc.     

Is specialization an evolutionary dead end? Testing for differences in speciation,extinction and trait transition rates across diverse phylogenies of specialists and generalists

Specialization has often been claimed to be an evolutionary dead end, with specialist lineages having a reduced capacity to persist or diversify. In a phylogenetic comparative framework, an evolutionary dead end may be detectable from the phylogenetic distribution of specialists, if specialists rarely give rise to large, diverse clades. Previous phylogenetic studies of the influence of specialization on macroevolutionary processes have demonstrated a range of patterns, including examples where specialists have both higher and lower diversification rates than generalists, as well as examples where the rates of evolutionary transitions from generalists to specialists are higher, lower or equal to transitions from specialists to generalists. Here, we wish to ask whether these varied answers are due to the differences in macroevolutionary processes in different clades, or partly due to differences in methodology. We analysed ten phylogenies containing multiple independent origins of specialization and quantified the phylogenetic distribution of specialists by applying a common set of metrics to all datasets. We compared the tip branch lengths of specialists to generalists, the size of specialist clades arising from each evolutionary origin of a specialized trait and whether specialists tend to be clustered or scattered on phylogenies. For each of these measures, we compared the observed values to expectations under null models of trait evolution and expected outcomes under alternative macroevolutionary scenarios. We found that specialization is sometimes an evolutionary dead end: in two of the ten case studies (pollinator‐specific plants and host‐specific flies), specialization is associated with a reduced rate of diversification or trait persistence. However, in the majority of studies, we could not distinguish the observed phylogenetic distribution of specialists from null models in which specialization has no effect on diversification or trait persistence.     

Loudness of birdsong is related to the body size,syntax and phonology of passerine species

Songs of passerines are generally complex, long‐range acoustic signals, and are highly diverse across species. This diversity must nevertheless be shaped by the capabilities of the avian vocal physiology. For example, within species, loudness has been shown to trade‐off with aspects of song complexity. Here, I ask if such trade‐offs with loudness influenced the evolutionary diversification of song among passerines. Comparing perceived song loudness across > 140 European and North American species showed that loudness is positively related to body size and to singing with simple trilled syntax, and negatively related to aspects of syllable complexity. Syntax and syllable phonology together explained more variation than body size did, indicating that the acoustic design of songs is an important factor determining loudness. These results show for the first time that loudness covaries with, and possibly limits, song complexity across species, suggesting that a trade‐off with loudness shaped the evolutionary diversification of passerine song.     

Causes of the latitudinal gradient in birdsong complexity assessed from geographical variation within two Himalayan warbler species

Aspects of birdsong complexity, such as the number of distinct notes in a song, commonly increase along latitudinal gradients, a pattern for which at least 10 explanations have been suggested. In two Himalayan warblers, songs are more complex in the northwest than in the southeast. In Grey‐hooded Warbler Phylloscopus xanthoschistos, high complexity results from increased note diversity within song types, sung across a higher bandwidth. In Blyth's Leaf Warbler Phylloscopus reguloides, high complexity is a consequence of increased variation between song types. The hypothesis with strongest support is that songs evolved to be more complex in species‐poor, demonstrably less noisy environments. We consider geographical variation to be an outcome of sexual selection favouring complexity across environments, where detection of the signal varies. Sexual selection favouring complexity may be resolved in different ways, because complexity has multiple features (repertoire size, song switching, etc.). We argue this has led to the great diversity in song that we have documented among five Phylloscopus species.     

Phylogenetic and compositional diversity are governed by different rules: a study of fleas parasitic on small mammals in four biogeographic realms

We studied patterns of phylogenetic and compositional diversity of fleas parasitic on small mammals and asked whether these patterns are affected by environmental variation or evolutionary/historical processes. We considered environmental variation via both off‐host (air temperature, precipitation, the amount of green vegetation, latitude) and host‐associated (phylogenetic and species composition) environments. The indicators of evolutionary/historical processes were phylogenetic and compositional uniqueness estimated via phylogenetic or compositional, respectively, β‐diversity of either fleas or hosts. We found that phylogenetic uniqueness of flea assemblages was the main predictor of their phylogenetic diversity in all realms. In addition, host phylogenetic diversity and uniqueness played also some role in the Palearctic, whereas the effect of the off‐host environment was either extremely weak or absent. Compositional diversity of fleas was consistently affected by compositional diversity of hosts in all realms except the Neotropics. The effect of the off‐host environment on compositional flea diversity was substantial in all realms except the Palearctic. No effect of latitude on either metric of flea diversity was found. We conclude that phylogenetic diversity of fleas is driven mainly by evolutionary/historical processes, whereas drivers of their compositional diversity are associated with current ecological conditions.     

Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae)

Aim The causes of geographical variation in species richness in clades that do not follow the latitudinal diversity gradient have rarely been investigated. Here, we examine spatial asymmetries of diversity in Gladiolus (Iridaceae), a large genus (> 260 species) that is present in two mediterranean climate biomes: the Cape of southern Africa (106 species) and the Mediterranean Basin (7 species). Despite convergence of climatic conditions between the two regions, the species density of Gladiolus is over one order of magnitude higher in the Cape than in the Mediterranean Basin. We investigate whether the diversity disparities observed in the genus are better explained by recent colonization of species‐poor areas (temporal hypothesis) or by differential rates of diversification (evolutionary hypothesis). Location Africa, Madagascar and Eurasia Methods We employ a recently developed Bayesian method for the estimation of diversification rates and a biogeographical optimization approach within a phylogenetic framework. Results In Gladiolus, the ‘diversity anomaly’ between the two Mediterranean climate regions cannot be explained solely by the time available for speciation in the Cape, but is also due to locally reduced rates of diversification in the Mediterranean Basin. Furthermore, high overall diversity in southern Africa stems from an ancient origin in the Cape allied with high rates of diversification in the summer‐rainfall region of the subcontinent. Main conclusions Both evolutionary and temporal hypotheses must be taken into account in order to explain the diversity anomaly between the Mediterranean Basin and the Cape. Our results suggest that regions at comparable latitudes and/or with similar climate may not converge in diversity levels due to heterogeneity of diversification rates and contrasting biogeographical histories.