Paleontological Patterns, Macroecological Dynamics and the Evolutionary Process

Here we consider evolutionary patterns writ large in the fossil record. We argue that Darwin recognized but downgraded or de-emphasized several of these important patterns, and we consider what a renewed emphasis on these patterns can tell us about the evolutionary process. In particular, one of the key patterns we focus on is the role geographic isolation plays in fomenting evolutionary divergence; another one of the key patterns is stasis of species; the final pattern is turnovers, which exist at several hierarchical scales, including regional ecosystem replacement and pulses of speciation and extinction. We consider how each one of these patterns are related to the dynamic of changing ecological and environmental conditions over time and also investigate their significance in light of other concepts including punctuated equilibria and hierarchy theory. Ultimately, we tie each of these patterns into a framework involving macroecological dynamics and the important role environmental change plays in shaping evolution from the micro- to macroscale.     

Progressive invasion and allopatric speciation can also explain distribution patterns of rock-dwelling cichlids from southern Lake Victoria: a comment on Seehausen and van Alphen (1999)

I show that distribution patterns of rock-dwelling haplochromine cichlids in the south-eastern part of Lake Victoria can be explained by allopatric speciation alone. Observed patterns are consistent with a progressive invasion of different lineages from older ( = deeper) parts of the lake, after which some lineages speciate more frequently than others. Based on a quantitative analysis of distribution data, Seehausen and van Alphen conclude that a high percentage of sympatric speciation (17.5%) is essential to explain the patterns. In my view this conclusion has its origins in an unjustifiable assumption. Seehausen and van Alphen assume that the unresolved phylogeny is balanced. However, allopatric speciation would typically result in imbalanced phylogenies.     

The Evolution of Avian Senescence Patterns: Implications for Understanding Primary Aging Processes

SYNOPSIS. The long life spans of birds relative to those ofmammals are intriguing to biogerontologists, particularly inlight of birds' high body temperatures, high blood glucose levels,and high metabolic rates—all of which should theoreticallyincrease their biochemical liability for rapid aging. The comparativelongevity of birds and other flying homeotherms is consistentwith evolutionary senescence theory, which posits that specieswith low mortality rates from predation or accident will bereleased from selection for rapid maturity and early reproduction,and will exhibit retarded aging. Comparative analyses of avianlife history parameters to date, although not as extensive asthose for mammals, broadly support an association between lowmortality rates, slow reproduction, and long lifespan. The diversityof bird life histories suggests the importance of developinga diversity of avian models for studies of aging mechanisms,both proximate and ultimate, and for using wild as well as domesticrepresentatives. Birds studied in the laboratory thus far showmany of the same manifestations of aging as mammals, includinghumans, and many ornithologists are beginning to document actuarialevidence consistent with aging in their study populations. Weencourage greater communication and collaboration among comparativegerontologists and ornithologists, in the hope that the studyof aging in birds will lead to an integrated understanding ofphysiological aging processes well grounded in an evolutionaryparadigm.     

Introduction. Antarctic ecology: from genes to ecosystems. Part 2. Evolution, diversity and functional ecology

The Antarctic biota has evolved over the last 100 million years in increasingly isolated and cold conditions. As a result, Antarctic species, from micro-organisms to vertebrates, have adapted to life at extremely low temperatures, including changes in the genome, physiology and ecological traits such as life history. Coupled with cycles of glaciation that have promoted speciation in the Antarctic, this has led to a unique biota in terms of biogeography, patterns of species distribution and endemism. Specialization in the Antarctic biota has led to trade-offs in many ecologically important functions and Antarctic species may have a limited capacity to adapt to present climate change. These include the direct effects of changes in environmental parameters and indirect effects of increased competition and predation resulting from altered life histories of Antarctic species and the impacts of invasive species. Ultimately, climate change may alter the responses of Antarctic ecosystems to harvesting from humans. The unique adaptations of Antarctic species mean that they provide unique models of molecular evolution in natural populations. The simplicity of Antarctic communities, especially from terrestrial systems, makes them ideal to investigate the ecological implications of climate change, which are difficult to identify in more complex systems.     

Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life

Summary The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family 1) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family 11) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotesin distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree. Offprint requests to: B. Labedan     

The Role of Adaptation to Host Plants in the Evolution of Reproductive Isolation: Negative Evidence from Tetranychus Urticae Koch

Reproductive isolation between demes of a phytophagous arthropod population that use different host plant species could evolve in two different ways. First, adaptation to different host species might result in reproductive isolation as a pleiotropic by-product. Second, if adaptation to one host species strongly reduces fitness on others, selection could favour mechanisms, such as host fidelity and assortative mating, that restrict gene flow between host-adapted demes. A laboratory selection experiment on the broadly polyphagous spider mite Tetranychus urticae gave information on these possibilities. A population allowed to adapt to tomato plants showed increased survival, development rate and fecundity on tomato relative to the base population from which it was derived. In spite of the large difference between the tomato-adapted and base populations in performance on tomato plants, the two populations showed no evidence of reproductive isolation, as measured by the hatching rate of eggs laid by F1 hybrids between the lines. Furthermore, a genetically variable population formed by hybridizing the tomato-adapted and base populations did not show evidence for a decline in ability to survive on tomato after more than ten generations of mass rearing on lima bean, indicating that tomato-adapted genotypes suffered little or no selective disadvantage on bean. These results give no support for the role of host plants in the evolution of reproductive isolation in T. urticae.     

Substrate Size and Primate Forelimb Mechanics: Implications for Understanding the Evolution of Primate Locomotion

International Journal of Primatology - Did the anatomical and locomotor specializations of primates evolve in response to requirements of locomotion and foraging on thin branches? Laboratory...     

Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

A direct attack on the protein-folding problem has been initiated with the free energy perturbation methods of molecular dynamics. The complete conformational probability map for the alanine dipeptide is presented. This work uses the SPC model for the explicit hydration of the dipeptide. Free energy differences for the four observed minima (beta, alpha R, alpha L, C7ax) are given, and the free energy barriers between minima are outlined.     

Allopolyploidization lays the foundation for evolution of distinct populations: evidence from analysis of synthetic Arabidopsis allohexaploids

Polyploidization is an important mechanism for introducing diversity into a population and promoting evolutionary change. It is believed that most, if not all, angiosperms have undergone whole genome duplication events in their evolutionary history, which has led to changes in genome structure, gene regulation, and chromosome maintenance. Previous studies have shown that polyploidy can coincide with meiotic abnormalities and somatic cytogenetic mosaics in Arabidopsis allotetraploids, but it is unclear whether this phenomenon can contribute to novel diversity or act as a mechanism for speciation. In this study we tested the hypothesis that mosaic aneuploidy contributes to the formation of incipient diversity in neoallopolyploids. We generated a population of synthesized Arabidopsis allohexaploids and monitored karyotypic and phenotypic variation in this population over the first seven generations. We found evidence of sibling line-specific chromosome number variations and rapidly diverging phenotypes between lines, including flowering time, leaf shape, and pollen viability. Karyotypes varied between sibling lines and between cells within the same tissues. Cytotypic variation correlates with phenotypic novelty, and, unlike in allotetraploids, remains a major genomic destabilizing factor for at least the first seven generations. While it is still unclear whether new stable aneuploid lines will arise from these populations, our data are consistent with the notion that somatic aneuploidy, especially in higher level allopolyploids, can act as an evolutionary relevant mechanism to induce rapid variation not only during the initial allopolyploidization process but also for several subsequent generations. This process may lay the genetic foundation for multiple, rather than just a single, new species.     

New Radiometric Ages for the BH-1 Hominin from Balanica (Serbia): Implications for Understanding the Role of the Balkans in Middle Pleistocene Human Evolution

Newly obtained ages, based on electron spin resonance combined with uranium series isotopic analysis, and infrared/post-infrared luminescence dating, provide a minimum age that lies between 397 and 525 ka for the hominin mandible BH-1 from Mala Balanica cave, Serbia. This confirms it as the easternmost hominin specimen in Europe dated to the Middle Pleistocene. Inferences drawn from the morphology of the mandible BH-1 place it outside currently observed variation of European Homo heidelbergensis. The lack of derived Neandertal traits in BH-1 and its contemporary specimens in Southeast Europe, such as Kocabaş, Vasogliano and Ceprano, coupled with Middle Pleistocene synapomorphies, suggests different evolutionary forces acting in the east of the continent where isolation did not play such an important role during glaciations.     

Mate choice and the genetic basis for colour variation in a polymorphic dart frog: inferences from a wild pedigree

Understanding how reproductive barriers evolve during speciation remains an important question in evolution. Divergence in mating preferences may be a common first step in this process. The striking colour pattern diversity of strawberry dart frog (Dendrobates pumilio) populations has likely been shaped by sexual selection. Previous laboratory studies have shown that females attend to male coloration and prefer to court with males of their own colour, suggesting that divergent morphs may be reproductively isolated. To test this hypothesis, we used molecular data to estimate pedigree relationships from a polymorphic population. Whereas in the laboratory both red and yellow females preferred to court with males of their own phenotype, our pedigree shows a pattern of assortative mating only for red females. In the wild, yellow females appear to be less choosy about their mates, perhaps because they incur higher costs associated with searching than females of the more common red phenotype. We also used our pedigree to investigate the genetic basis for colour-pattern variation. The phenotype frequencies we observed were consistent with those expected if dorsal background coloration is controlled by a single locus, with complete dominance of red over yellow. Our results not only help clarify the role of sexual selection in reducing gene flow, but also shed light on the mechanisms underlying colour-pattern variation among sympatric colour morphs. The difference we observed between mating preferences measured under laboratory conditions and the pattern of mate choice observed in the wild highlight the importance of field studies for understanding behavioural reproductive isolation.     

Female choice in Drosophila: evidence from Hawaii and implications for evolutionary biology

Details of female choice of mate in Drosophila silvestris of Hawaii strikingly parallels epigamic behavioral systems in many other animals and may be common in other species of Drosophilidae. Females respond selectively to male circling, wing displays, songs and tactile stimulation with foreleg cilia, a quantitative character that is highly variable in some populations. I hypothesize that the female can exert choice based on these cues from individual males that differ genetically by quantitative trait loci. Laboratory tests show that one third of courting males are repeatedly rejected in favor of a minority of alpha males. This result imposes non-random mating at the local population level. Past multiple-choice lab tests, widely used to measure isolation between pairs of populations or species of Drosophila may be flawed, since random mating has been assumed in the interpretation of results. Pre-mating sexual selection is clearly a powerful intrapopulation force in population biology. This view creates difficulties for discerning any proposed simultaneous interpopulation selective events in the presence of strong female choice. The long-held theory assuming that there is significant selection for pre-mating isolation between groups is questionable.     

Research Needs for Understanding and Predicting the Behavior of Managed Ecosystems: Lessons from the Study of Agroecosystems

Managed ecosystems are complex, dynamic systems with spatially varying inputs and outputs that are the result of interrelated physical, biological, and human decision-making processes. To gain an adequate understanding of these systems and predict their behavior, we believe that it is necessary to move beyond stylized theoretical models and loosely coupled disciplinary simulation models to what we describe as “fully integrated models.” Herein we present a conceptual framework for a more integrated approach to the study of managed ecosystems using the example of agricultural ecosystems. We then propose the implementation of a research agenda that fosters coordinated disciplinary research aimed at a better understanding and quantification of linkages across disciplinary models. Key research issues include the effects of spatial scale, the assessment of uncertainty in coupled models, and methods for collecting and analyzing spatially referenced data. Received 6 October 2000; accepted 10 April 2001.     

Evolution of human mitochondrial DNA: Evidence for departure from a pure neutral model of populations at equilibrium

Summary Human mitochondrial DNA (mtDNA) data from 18 populations have been carefully reexamined. A phylogeny of 77 mtDNA types found among the 1389 individuals analyzed for restriction fragment length polymorphisms (RFLPs) was established using the parsimony principle and compared to a UPGMA tree of the 18 populations. Both analyses agreed in separating African samples from the other populations, though the mtDNA type phylogeny suggested close relations between Africans and other continental groups. Conformity of observed mtDNA type frequency distributions with the infinite allele model was studied for 31 human populations. Several Oriental and Caucasoid populations were found to be overly homogeneous, generally due to an elevated frequency of one particular type. Contrastingly, all African samples conformed to the neutral model of populations at equilibrium and presented more diversified distributions. This suggested that part of the apparent African divergence was due to heterogeneous evolutionary processes and confirmed that some diversity reducing factors were at work in Caucasoids and Orientals. Several nonexclusive hypotheses accounting for the rejection of the neutrality tests were discussed. Alternative hypotheses concerning modern human emergence were also reviewed in the light of present results.     

A comparative study of allozyme variation of peripheral and central populations of Silene nutans L. (Caryophyllaceae) from Western Europe: implications for conservation

In Belgium, at the western border of its continental distribution range, the perennial herb S. nutans has evolved two parapatric ecotypes (calcicolous or silicicolous), which show contrasted allozyme, morphological and adaptive patterns, and isolating reproductive barriers. We examined allozyme variation in 21 populations close to Belgium (from France and Luxemburg) in relation to their peripheral or central geographical position, and investigated their genetic relationships with the Belgian ecotypes. Both peripheral and central populations showed high genetic variation. They were differentiated from each other, but not in relation to the substrate (calcareous or siliceous). The peripheral and central populations were related to the Belgian silicicolous and calcicolous ecotype, respectively. This suggests an ancient differentiation and different past histories for the Belgian ecotypes, and parapatric speciation processes. This study exemplifies the high evolutionary potential of populations at range peripheries and the need for considering them in conservation strategies.     

Evolution of Receptors for Growth Hormone and Somatolactin in Fish and Land Vertebrates: Lessons from the Lungfish and Sturgeon Orthologues

Two cognate hormones, growth hormone (GH) and somatolactin (SL), control several important physiological processes in vertebrates. Knowledge about GH and its receptor (GHR) has accumulated over the last decades. However, much less is known about SL and its receptor (SLR). SL is found only in fish (including lungfish), suggesting that it was present in the common ancestor of vertebrates, but was lost secondarily in the lineage leading to land vertebrates after the lungfish branched off. SLR was suggested to be a duplicated copy of GHR acquired only in teleosts via the fish-specific genome duplication (FSGD). This scenario (i.e., the existence of SL but not SLR in the vertebrate ancestors) is intriguing but contested. In this study, we first evaluated the plausibility of this scenario through synteny analyses and found that the loci for GHR and SLR are located in syntenic genomic positions, whereas the loci for GH and SL are not. Next, we cloned GHRs of lungfish and sturgeon, which possess SL but did not undergo the FSGD (i.e., they should not possess SLR). Their phylogenetic positions in the GHR/SLR gene tree further support the fish-specific scenario for the GHR–SLR duplication. Interestingly, their sequences share greater similarity with teleost SLRs and reptilian/amphibian GHRs than with the GHRs of mammals, birds, and teleosts. On the basis of these results, we discuss the validity of the nomenclature of the teleost-specific copy of GHR as SLR and an ancestral receptor(s) for SL before the evolution of SLR during the FSGD.     

Highly Conserved Caspase and Bcl-2 Homologues from the Sea Anemone Aiptasia pallida: Lower Metazoans as Models for the Study of Apoptosis Evolution

Key insight into the complexities of apoptosis may be gained from the study of its evolution in lower metazoans. In this study we describe two genes from a cnidarian, Aiptasia pallida, that are homologous to key genes in the apoptotic pathway from vertebrates. The first is a novel ancient caspase, acasp, that displays attributes of both initiator and executioner caspases and includes a caspase recruitment domain (CARD). The second, a Bcl-2 family member, abhp, contains a BH1 and BH2 domain and shares structural characteristics and phylogenetic affinity with a group of antiapoptotic Bcl-2s including A1 and Bcl-2L10. The breadth of occurrence of other invertebrate homologues across the phylogenetic trees of both genes suggests that the complexity of apoptotic pathways is an ancient trait that predates the evolution of vertebrates and higher invertebrates such as nematodes and flies. This paves the way for establishing new lower metazoan model systems for the study of apoptosis. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Stuart Newfeld]