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PubMed2002

The probability of topological concordance of gene trees and species trees.

The concordance of gene trees and species trees is reconsidered in detail, allowing for samples of arbitrary size to be taken from the species. A sense of concordance for gene tree and species tree topologies is clarified, such that if the "collapsed gene tree" produced by a gene tree has the same topology as the species tree, the gene tree is said to be topologically concordant with the species tree. The term speciodendric is introduced to refer to genes whose trees are topologically concordant with species trees. For a given three-species topology, probabilities of each of the three possible collapsed gene tree topologies are given, as are probabilities of monophyletic concordance and concordance in the sense of N. Takahata (1989), Genetics 122, 957-966. Increasing the sample size is found to increase the probability of topological concordance, but a limit exists on how much the topological concordance probability can be increased. Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation.

Biological Evolution↗
PubMed2025

Mapping Species Birth Across the Recombination Landscapes of Marine Snails.

Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.

Genetic Introgression↗
PubMed1996

Population dynamic models generating the lognormal species abundance distribution.

This paper deals with a new class of stochastic species abundance models where the abundances are the points of an inhomogeneous Poisson process. These models are the result of a dynamic approach in which the changes in abundances through time are described by a multivariate diffusion and speciation constitutes a homogeneous Poisson process. In particular, the lognormal model is generated by assuming that the density regulation within each species is given by the Gompertz curve and that the environmental variances are constant. A substantial generalization is obtained by introducing a general type of interspecific density regulation and correlated environmental noise. This more general mechanism also generates the lognormal species abundance distribution.

Animals↗
PubMed2005

When morphometry meets genetics: inferring the phylogeography of Carabus solieri using Fourier analyses of pronotum and male genitalia.

Population differentiation is a crucial step in the speciation process and is therefore a central subject in studies of microevolution. Assessing divergence and inferring its dynamics in space and time generally require a wide array of markers. Until now however, most studies of population structure are based on molecular markers and those concerning morphological traits are more scarce. In the present work, we studied morphological differentiation among populations of the ground beetle Carabus solieri, and tested its congruence with genetic population structure. The shape of pronotum and aedeagus was assessed using Dual Axis Fourier Shape Analysis. manova on Fourier coefficients revealed highly significant morphological variation between populations and a similar geographical pattern of differentiation for both structures. On the whole, morphological and genetic patterns were also found to be congruent. Our analysis confirms the phylogeographical scenario proposing that two entities of C. solieri differentiated during the last glaciation events before recolonizing the actual range of the species. It also indicates a large introgression between the two differentiated entities in the centre of the range.

Analysis of Variance↗
PubMedDate not supplied

[Progress of ecological parasitology--parasite communities].

Many of the major development in the field of parasite community ecology have been due to a switch in focus from a search for pattern to investigation of the processes that produce those patterns. This switch has been accompanied by a recognition that different processes operate at the scale of the individual host (processes determining host specificity and attributes of the niches of the parasites), within the unit of habitat (processes determining population dynamics, exchange of parasites, and transmission), and among units of habitat (processes determining colonization, extinction, or local speciation of parasites). Further developments are likely to depend upon the coordinated use of models, experimental approaches, and field observations aimed at clarifying the conditions under which the processes at each scale became particularly important.

Animals↗
PubMed1995

A genetical theory of species selection.

Species selection, differential rates of speciation or extinction resulting from species level characters, is often invoked as the main mechanism of macroevolution that is not simply an extension of microevolutionary processes. So long as we are careful in defining "species", the logic of species selection is sound. This does not mean, however, that this process can influence evolutionary dynamics under realistic conditions. The principal challenge to the efficacy of species selection as an evolutionary mechanism is the idea that selection between individuals within species will be so much more efficient as to swamp out any effects of selection between species. To assess this, a genetic model is constructed that includes simultaneous selection within and between species, and this is used to ask: under what conditions could species selection influence evolutionary dynamics, even in the face of opposing selection between individuals? The model shows that the efficacy of species selection is strongly determined by the time between speciation events (measured in individual generations), the mutation rate of the character under consideration, and the initial size of a newly formed reproductively isolated population. Data indicate that a few studied lineages have shown sufficiently high speciation rates to make species selection an important mechanism in the evolution of characters with mutation rates on the order of 10(-6) per generation. Quantitative characters, such as body size, generally change too readily for species selection to be relevant to their evolution. Complex characters, however, may be good candidates to be influenced by species selection. The interaction of selection within and between species can be subtle, with individual selection looking, from the standpoint of a species, very much like development of an individual. Furthermore, selection between individuals may be the main process assembling complex adaptations, while species selection allows them to persist over long periods of time.

Animals↗
PubMed2006

Assessing latitudinal gradients in speciation rates and biodiversity at the global scale.

The mechanisms responsible for latitudinal biodiversity gradients have fascinated and perplexed biologists since the time of Darwin. Ecological theory has yielded two general classes of mechanisms to account for variation in biodiversity: dispersal-assembly mechanisms that invoke differences in stochastic rates of speciation, extinction and dispersal; and niche-assembly mechanisms that invoke species differences, species interactions and environmental heterogeneity. Distinguishing between these two classes of mechanisms requires explicit consideration of macroevolutionary dynamics. Here, we assess the importance of dispersal-assembly mechanisms in the origin and maintenance of biodiversity using fossil data that encompass 30 million years of macroevolution for three distinct groups of ocean plankton: foraminifera, nannoplankton and radiolaria. Applying new methods of analysis to these fossil data, we show here for the first time that latitudinal biodiversity gradients exhibit strong positive correlations with speciation rates even after explicitly controlling for variation in sampling effort and for increases in habitat area towards the equator. These findings provide compelling evidence that geographical variation in macroevolutionary dynamics is a primary determinant of contemporary biodiversity gradients, as predicted by dispersal-assembly theory.

Animals↗
PubMed2001

Dynamic colloid--water partitioning of pyrene through a coastal Baltic spring bloom.

Colloidal organic particles constitute the dominant portion of particulate organic matter in surface seawater, but their influence on the phase speciation and bioavailability of hydrophobic organic compounds (HOCs) is sparsely evaluated. Studies on colloid-water partitioning have been focused on other regimes and have largely been performed on chemically defined subportions of total colloids such as the humic fraction. Available estimates of colloid-water partition coefficients (Kcoc) are highly variable and not easily explained by regularly applied Kow-Koc relationships. Here, pyrene was partitioned to bulk natural colloids isolated using cross-flow ultrafiltration techniques from the surface water of a coastal bay. A key objective was to elucidate biogeochemical controls on the changing colloid-sorbent qualities over the course of the dynamic allochtonous-autochtonous transition of a well-constrained boreal coastal spring bloom. The pyrene Kcoc was found to decrease from 12.9+/-0.9 x 10(3) Lw/kg(oc) in the terrestrial runoff dominated regime to values around 2.9+/-0.7 x 10(3) Lw/kg(oc), once phytoplankton production became the governing source of organic matter to the surface waters. The changing Kcoc was well correlated with the molar extinction coefficient at 280 nm of the colloidal organic carbon. This study supports other reports of an improved prediction of HOC phase speciation through this simple molecular proxy of the "quality" of organic sorbents. While being poor sorbents on a carbon atom basis, relative to soils and sediments, coastal marine colloids, by their shear abundance, may significantly attenuate the truly dissolved exposures of HOCs with log Kow above 5.

Absorption↗
PubMed2004

Neutral theory: the stability of forest biodiversity.

The unified neutral theory of biodiversity and biogeography provides a dynamic null hypothesis for the assembly of natural communities. It is also useful for understanding the influence of speciation, extinction, dispersal and ecological drift on patterns of relative species abundance, species-area relationships and phylogeny. Clark and McLachlan argue that neutral drift is inconsistent with the palaeorecord of stability in fossil pollen assemblages of the Holocene forests of southern Canada. We show here that their analysis is based on a partial misunderstanding of neutral theory and that their data alone cannot unambiguously test its validity.

Biodiversity↗
PubMed2006

Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands.

Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Réunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.

Animal Migration↗
PubMed2006

Reproductive isolation between Pogonomyrmex rugosus and two lineages with genetic caste determination.

Hybrid speciation occurs when combination of two interspecific genomes results in individuals that are of high fitness but reproductively incompatible with the parental species. Although hybrid speciation is a relatively common source of new species in plants, it appears to be a much rarer occurrence in animal taxa. Here we report on reproductive isolation and range overlap between the rough harvester ant Pogonomyrmex rugosus and two lineages with hybrid genotypes (H 1 and H2). Both lineages obligately interbreed and produce genetically distinct queen and worker offspring, a phenomenon referred to as genetic caste determination (GCD). Diploid offspring produced by gametes of the same lineage develop only into queens, whereas diploid offspring derived from gametes of distinct lineages develop into workers. We investigated small-scale patterns of gene flow between the parent and the two H lineages by sampling along an 80-km transect between a pure P. rugosus population and a two-lineage population. Microsatellite and mitochondrial markers both indicated virtually no gene flow between the parent species and either lineage even at sites where parental and H-lineage colonies co-occurred. The geographic ranges of the parental species and the two-lineage population were essentially parapatric, with a surprisingly narrow band of overlap and evidence of spatial structuring even at microgeographic scales within the transition zone. This suggests that ecological competition with the parent species plays a significant role in determining the evolutionary persistence and current distribution of the hybrid lineages and the genetic caste system.

Animals↗
PubMed2006

A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia).

To explore the evolutionary consequences of climate-induced fluctuations in distribution of rainforest habitat we contrasted demographic histories of divergence among three lineages of Australian rainforest endemic skinks. The red-throated rainbow skink, Carlia rubrigularis, consists of morphologically indistinguishable northern and southern mitochondrial DNA (mtDNA) lineages that are partially reproductively isolated at their parapatric boundary. The third lineage (C. rhomboidalis) inhabits rainforests just to the south of C. rubrigularis, has blue, rather than red-throated males, and for mtDNA is more closely related to southern C. rubrigularis than is northern C. rubrigularis. Multigene coalescent analyses supported more recent divergence between morphologically distinct lineages than between morphologically conservative lineages. There was effectively no migration and therefore stronger isolation between southern C. rubrigularis and C. rhomboidalis, and low unidirectional migration between morphologically conservative lineages of C. rubrigularis. We found little or no evidence for strong differences in effective population size, and hence different contributions of genetic drift in the demographic history of the three lineages. Overall the results suggest contrasting responses to long-term fluctuations in rainforest habitats, leading to varying opportunities for speciation.

Animals↗
PubMed2000

Geographic range size and evolutionary age in birds.

Together with patterns of speciation and extinction, post-speciation transformations in the range sizes of individual species determine the form of contemporary species range-size distributions. However, the methodological problems associated with tracking the dynamics of a species' range size over evolutionary time have precluded direct study of such range-size transformations, although indirect evidence has led to several models being proposed describing the form that they might take. Here, we use independently derived molecular data to estimate ages of species in six monophyletic groups of birds, and examine the relationship between species age and global geographic range size. We present strong evidence that avian range sizes are not static over evolutionary time. In addition, it seems that, with the regular exception of certain taxa (for example island endemics and some threatened species), range-size transformations are non-random in birds. In general, range sizes appear to expand relatively rapidly post speciation; subsequently; and perhaps more gradually, they then decline as species age. We discuss these results with reference to the various models of range-size dynamics that have been proposed.

Animals↗
PubMed2026

Recurrent hybridization shapes the diversification of Western Palearctic common toads (Bufo bufo complex).

Glacial cycles repeatedly fragmented temperate species into refugial populations, fostering divergence as a first stage towards speciation. Yet, interglacial expansions often reconnected these lineages, allowing gene flow to erode differentiation and reshape phylogeographic trajectories. We investigate these dynamics in Western Palearctic common toads (Bufo bufo complex), integrating genome-wide ddRAD-seq loci with an extensive mitochondrial dataset. Phylogenomic analyses resolved the three recognized species B. eichwaldi, B. spinosus and B. bufo, and within the latter, four major lineages distributed across the Apennine Peninsula, the Balkans, the Caucasus, and northern Europe. Mitochondrial and nuclear patterns were deeply discordant, and different approaches of historical gene flow inferences all supported past hybridization. In particular, our analyses suggest that the Caucasian population, previously attributed to the disputed species "B. verrucosissimus" based on its deeply divergent mtDNA, represents a shallow nuclear lineage within B. bufo and forms a broad intergradation zone with the Balkan lineage in Anatolia, arguing against a species status. Altogether, these results highlight a recurrent process in which refugial lineages do not diverge in strict isolation but repeatedly experience gene flow, thus reducing opportunities to speciate, and blurring tree-based phylogeographic and systematic hypotheses.

Amphibia↗
PubMed2000

Evolution of genetic codes through isologous diversification of cellular states.

Evolution of genetic codes is studied as change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for a choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA - amino acid complexes in a cell is introduced and studied numerically. It is shown that the biochemical states of cells are differentiated by cell-cell interactions, and each differentiated type starts to use a different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. The relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes; later, with mutation in the genotype, the genotype also differentiates into discrete types, while maintaining the "symbiotic" relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.

Biological Clocks↗
PubMed2002

The role of mercury redox reactions in snow on snow-to-air mercury transfer.

Wet deposition of Hg in snow represents a major air-to-land flux of Hg in temperate and polar environments. However, the chemical speciation of Hg in snow and its chemical and physical behavior after deposition are poorly understood. To investigate Hg dynamics in snow, we followed Hg0 and total Hg concentrations in a snowpack above a frozen lake over 1 month. Our results indicate that newly deposited Hg is highly labile in snowpacks. On average, Hg levels in particular snow episodes decrease by 54% within 24 h after deposition. We hypothesize that Hg depletion in snow could be caused by a rapid snow-to-air Hg transfer resulting from Hg(II) photoinduced reduction to volatile Hg0. Both snowmelt incubated under a UV lamp at 17 degrees C and solid snow incubated under the sun at -10 degrees C in clear reaction vessels yielded a statistically significant increase in Hg0(aq) with time of exposure, while the Hg0(aq) levels remained constant in the dark controls. The snow-to-air Hg transfer we observed in this study suggests that the massive Hg deposition events observed in springtime in northern environments may have less impact than previously anticipated, since once deposited, Hg could be rapidly reduced and re-emitted.

Air↗