Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective

The eastern Asian and eastern North American disjunction in Juglans offers an opportunity to estimate the time since divergence of the Eurasian and American lineages and to compare it with paleobotanical evidence. Five chloroplast DNA noncoding spacer (NCS) sequences: trnT−trnF, psbA−trnH, atpB−rbcL, trnV-16S rRNA, and trnS-trnfM and data from earlier studies (matK, ITS, and nuclear RFLP) were used to reconstruct phylogeny and to estimate the divergence time of major lineages. Seventeen taxa from four sections of Juglans and two outgroup taxa, Pterocarya stenoptera and Carya illinoiensis were included. NCS data was congruent only with matK data. Both maximum parsimony (MP) and maximum likelihood (ML) cladograms were concordant at the sectional level and revealed three well-supported monophyletic clades corresponding to sections Juglans, Cardiocaryon, and Rhysocaryon in both NCS and combined analyses. The single extant American butternut, Juglans cinerea was placed within the poorly resolved, but well-supported Rhysocaryon. Placement of taxa within Rhysocaryon and Cardiocaryon were inconsistent between NCS and combined analyses. Overall, the results suggest that: (1) the NCS sequence divergence observed within and between sections of Juglans is low and the addition of matK data only marginally improved resolution within Rhysocaryon; (2) the early divergence of section Juglans in both MP and ML analyses of NCS and combined data implies its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; and (3) the extant taxa may not hold the footprints to unravel the evolutionary history of the genus.     

Stabilité de l'espèce et évolution: La théorie de l'équilibre intermittent («Punctuated equilibrium)

Paleontologists' traditional conceptions on evolution do not seem to be in perfect accord with these of biologists. The gradual phyletism is compatible neither with E. Mayr's model of the Founder, nor with the actual stability of most of the paleontological species. The punctuated equilibrium model proposed by N. Eldredge & S.J. Gould offers a solution which integrates both paleontological observations and the data of modern biology.     

Le concept d'évolution polyphasée et ses implications

Analysis of allopatric speciation shows that it ispolyphased, each phase being characterized by populational and temporal modes organized into the following general sequence: phase 1 of desorganization of the gene pool; phase 2a of reorganization leading to reproductive isolation; phase 2b of adaptative reorganizational achievment. Depending on the circumstances, polyphased sequences are more or less complex and complete. Analysis of other models of speciation (Dumbbell, circular overlap, diachronic bottleneck) shows that anagenesis and cladogenesis can be no longer considered as two modes of evolution, they appear to be only patterns resulting in the occurrence of various modes of the sequential phases of speciation. Evolution appears as a result of species equilibria punctuated by desequilibria inducing polyphased sequences of various temporal and populational modes leading to new species equilibria through anagenetic or cladogenetic pattern. Phyletic gradualism versus punctualism polemics reflect distinct approaches by biologists and paleontologists at different integration levels and scales. In the new polyphasedsequence-speciation concept they are complementary in a coherent interacting system ensuring balance between species and environment.     

SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE

If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.     

DO PHYLOGENETIC METHODS PRODUCE TREES WITH BIASED SHAPES?

We examine whether phylogenetic methods provide biased estimates of tree shape with respect to the random branching model. We investigate the performance of five commonly used phylogenetic methods using computer simulation: (1) maximum parsimony; (2) neighbor joining; (3) UPGMA with an outgroup taxon; (4) UPGMA without an outgroup taxon; and (5) maximum likelihood. All methods provide estimates of tree shape that are, on average, more asymmetrical than the true tree, especially when rates of evolution are high. We suggest a simple explanation for the bias and propose a modified test of tree shape that corrects for it.     

PHYLOGENIES WITHOUT FOSSILS

Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.     

Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny

Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis-Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny.     

A comparative analysis of island floras challenges taxonomy‐based biogeographical models of speciation

Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy‐based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.     

PERSISTENCE OF WITHIN‐SPECIES LINEAGES: A NEGLECTED CONTROL OF SPECIATION RATES

We present a framework distinguishing three principal controls of speciation rate: rate of splitting, level of persistence, and length of speciation duration. We contend that discussions on diversification become clearer in the light of this framework, because speciation rate variation could be attributed to any of these controls. In particular, we claim that the role of persistence of within‐species lineages in controlling speciation rates has been greatly underappreciated. More emphasis on the persistence control would change expectations of the role of several biological traits and environmental factors, because they may drive speciation rate in one direction through the persistence control and in the opposite direction through the other two controls. Traits and environments have been little studied regarding their influence on speciation rate through the persistence control, with climatic fluctuations being a relatively well‐studied exception. Considering the recent advances in genomic and phylogenetic analysis, we think that the time is ripe for applying the framework in empirical research. Variation among clades and areas (and thus among traits and environments) in the importance of the three rate controls could be addressed for example by dating splitting events, detecting within‐species lineages, and scanning genomes for evidence of divergent selection.     

Reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in sympatry

• Reproductive isolation is a necessary condition for plant domestication in their domestication centre where crops co‐occur with their wild progenitors. However, the identification of reproductive barriers and their relative contribution to reproductive isolation have been overlooked in plants under domestication.
• We assessed pre‐ and post‐pollination reproductive barriers and their relative contribution to reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in its domestication centre.
• We found that wild and domesticated chaya both exhibit a high degree of reproductive isolation. However, the reproductive isolation barriers exhibited some asymmetry: while pre‐pollination barriers (differential pollen production and pollinator specificity) were only detected in wild plants, post‐pollination barriers (pollen–pistil incompatibility and/or failure to set fruit) were observed in both wild and domesticated plants.
• We conclude that complete reproductive isolation has evolved in sympatry in co‐occurring domesticated and wild chaya.