Dates from the molecular clock: how wrong can we be?

The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates

The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity. The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock. However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate. Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate. Here it is shown that the equidistance result remains valid even when different species can be independently shown to have different mutation rates. A random sampling of 50 proteins shows that nearly all proteins display the equidistance result despite the fact that many proteins have non-constant mutation rates. Therefore, the genetic equidistance result does not necessarily mean a constant mutation rate. Observations of different mutation rates do not invalidate the genetic equidistance result. New ideas are needed to explain the genetic equidistance result that must grant different mutation rates to different species and must be independently testable.

Origin and diversification of the clawed lobster genus Metanephrops (Crustacea: Decapoda: Nephropidae)

A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) but refutes monophyly of the other two groups (the arafurensis and thomsoni groups). The results in general support a recent morphology-based cladistic analysis of this genus except that this study suggests M. neptunus to be a basal rather than a derived species as indicated in the morphological analysis. This species is genetically diverse over its geographical range. Moreover, the two color forms of M. thomsoni are genetically distinct, most likely representing different species. The molecular phylogeny and current distribution pattern of the extant species, together with the fossil record, suggest that the genus originated in the Antarctica in the Cretaceous, followed by diversification and dispersal along the continental shelf of different continents as a result of the vicariant events associated with the breakup of the Southern Temperate Gondwana since Late Cretaceous.

Phylogenetic Approaches to the Study of Extinction

Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa.

Spread of an introduced vector-borne banana virus in Hawaii

Emerging diseases are increasing in incidence; therefore, understanding how pathogens are introduced into new regions and cause epidemics is of importance for the development of strategies that may hinder their spread. We used molecular data to study how a vector-borne banana virus, Banana bunchy top virus (BBTV), spread in Hawaii after it was first detected in 1989. Our analyses suggest that BBTV was introduced once into Hawaii, on the island of Oahu. All other islands were infected with isolates originating from Oahu, suggesting that movement of contaminated plant material was the main driving factor responsible for interisland spread of BBTV. The rate of mutation inferred by the phylogenetic analysis (1.4 x 10(-4) bp/year) was similar to that obtained in an experimental evolution study under greenhouse conditions (3.9 x 10(-4) bp/year). We used these values to estimate the number of infections occurring under field conditions per year. Our results suggest that strict and enforced regulations limiting the movement of banana plant material among Hawaiian islands could have reduced interisland spread of this pathogen.

Colloquium paper: phylogenetic trees and the future of mammalian biodiversity

Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerable to increased human pressure. We outline how the approach might be extended to consider future trends in anthropogenic drivers, to identify likely future battlegrounds of mammalian conservation, and the likely casualties. This framework could help to highlight consequences of choosing among different future climatic and socioeconomic scenarios. We end by discussing priority-setting, showing how alternative currencies for diversity can suggest very different priorities. We argue that aiming to maximize long-term evolutionary responses is inappropriate, that conservation planning needs to consider costs as well as benefits, and that proactive conservation of largely intact systems should be part of a balanced strategy.

The prehistory of potyviruses: their initial radiation was during the dawn of agriculture

BACKGROUND

Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other.

METHODS AND FINDINGS

We have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas.

CONCLUSIONS/SIGNIFICANCE

Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.15x10(-4) nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation.

DNA-sequence variation among Schistosoma mekongi populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis

Background

Schistosomiasis in humans along the lower Mekong River has proven a persistent public health problem in the region. The causative agent is the parasite Schistosoma mekongi (Trematoda: Digenea). A new transmission focus is reported, as well as the first study of genetic variation among S. mekongi populations. The aim is to confirm the identity of the species involved at each known focus of Mekong schistosomiasis transmission, to examine historical relationships among the populations and related taxa, and to provide data for use (a priori) in further studies of the origins, radiation, and future dispersal capabilities of S. mekongi.

Methodology/Principal Findings

DNA sequence data are presented for four populations of S. mekongi from Cambodia and southern Laos, three of which were distinguishable at the COI (cox1) and 12S (rrnS) mitochondrial loci sampled. A phylogeny was estimated for these populations and the other members of the Schistosoma sinensium group. The study provides new DNA sequence data for three new populations and one new locus/population combination. A Bayesian approach is used to estimate divergence dates for events within the S. sinensium group and among the S. mekongi populations.

Conclusions/Significance

The date estimates are consistent with phylogeographical hypotheses describing a Pliocene radiation of the S. sinensium group and a mid-Pleistocene invasion of Southeast Asia by S. mekongi. The date estimates also provide Bayesian priors for future work on the evolution of S. mekongi. The public health implications of S. mekongi transmission outside the lower Mekong River are also discussed.

Schistosomiasis is a disease caused by parasitic worms of the genus Schistosoma. In the lower Mekong river, schistosomiasis in humans is called Mekong schistosomiasis and is caused by Schistosoma mekongi. In the past, Mekong schistosomiasis was known only from the lower Mekong river. Here DNA-sequence variation is used to study the relationships and history of populations of S. mekongi. Populations from other rivers are compared and shown to be S. mekongi, thus confirming that this species is not restricted to only a small section of one river. The dates of divergence among populations are also estimated. Prior to this study it was assumed that S. mekongi originated in Yunnan, China, migrated southwards across Laos and into Cambodia, later becoming extinct in Laos (due to conditions unsuitable for transmission). In contrast, the dates estimated here indicate that S. mekongi entered Cambodia from Vietnam, 2.5–1 Ma. The pattern of genetic variation fits better with a more recent, and ongoing, northwards migration from Cambodia into Laos. The implications are that Mekong schistosomiasis is more widespread than once thought and that the human population at risk is up to 10 times greater than originally estimated. There is also an increased possibility of the spread of Mekong schistosomiasis across Laos.

How to summarize estimates of ancestral divergence times

The use of molecular sequence data has increased interest in trying to date evolutionary events, with researchers wanting both an estimate of the divergence time and a confidence interval for that estimate. However, two methodological issues have recently been raised with respect to precision of the estimates: (i) the time of the ancestral event is over-estimated; and (ii) the confidence interval is asymmetrical. I argue that if the estimates of divergence time are considered to be samples from a lognormal probability distribution, then this would explain both of these problems. This implies that divergence times should be presented using geometric means rather than arithmetic means, both for estimates and for their confidence intervals. I present analyses based on both computer simulations and empirical data to show that this approach is effective for both single-gene and multiple-gene data sets. Treating divergence time as a lognormal variable thus provides a simple unifying framework for dealing with many of the problems associated with the estimation of divergence (and possibly coalescence) times. Use of this approach (based on geometric means) can, unfortunately, lead to very different biological conclusions compared to the currently used calculation methods (based on arithmetic means).

Geographic variation in the advertisement call of Crinia signifera (Anura:Myobatrachidae) on Kangaroo Island and across southern south-eastern Australia

The male advertisement call of anuran amphibians has a major role in mate choice, and regional variation in this attribute can act as an indicator of speciation and a marker for genetic differentiation. As part of a regional study of geographic variation in the male advertisement call of Crinia signifera across south-eastern Australia and adjacent larger continental islands, samples of advertisement calls from two populations on Kangaroo Island and two populations on the adjacent Fleurieu Peninsula were compared. Four call attributes were considered: pulse number, call duration, pulse rate and dominant frequency. Pulse number is considered the most reliable for comparative purposes because it is not influenced by effective temperature or audio recording and analysis. The two island populations (central and eastern, ~24 km apart) differ significantly in pulse number, with contact but no overlap of interquartile ranges. The eastern sample differs markedly from those on the nearby Fleurieu Peninsula – which are both similar to the more distant central island sample. Geographic variation in pulse number in these four samples and 11 others from two recent publications is then interpreted in the light of land bridges and lower temperatures of the late Pleistocene and early Holocene.

Atmosphere, ecology and evolution: what drove the Miocene expansion of C(4) grasslands?

Grasses using the C(4) photosynthetic pathway dominate today's savanna ecosystems and account for approximately 20% of terrestrial carbon fixation. However, this dominant status was reached only recently, during a period of C(4) grassland expansion in the Late Miocene and Early Pliocene (4-8 Myr ago). Declining atmospheric CO(2) has long been considered the key driver of this event, but new geological evidence casts doubt on the idea, forcing a reconsideration of the environmental cues for C(4) plant success.Here, I evaluate the current hypotheses and debate in this field, beginning with a discussion of the role of CO(2) in the evolutionary origins, rather than expansion, of C(4) grasses. Atmospheric CO(2) starvation is a plausible selection agent for the C(4) pathway, but a time gap of around 10 Myr remains between major decreases in CO(2) during the Oligocene, and the earliest current evidence of C(4) plants.An emerging ecological perspective explains the Miocene expansion of C(4) grasslands via changes in climatic seasonality and the occurrence of fire. However, the climatic drivers of this event are debated and may vary among geographical regions.Uncertainty in these areas could be reduced significantly by new directions in ecological research, especially the discovery that grass species richness along rainfall gradients shows contrasting patterns in different C(4) clades. By re-evaluating a published data set, I show that increasing seasonality of rainfall is linked to changes in the relative abundance of the major C(4) grass clades Paniceae and Andropogoneae. I propose that the explicit inclusion of these ecological patterns would significantly strengthen climate change hypotheses of Miocene C(4) grassland expansion. Critically, they allow a new series of testable predictions to be made about the fossil record.Synthesis. This paper offers a novel framework for integrating modern ecological patterns into theories about the geological history of C(4) plants.

The genetics of mammalian invasions: a review

This review takes a broad perspective on mammalian invasions and considers genetic aspects of both natural colonisation and conservation-related translocations as a backdrop to the genetics of introductions of wildlife-management concern. Genetics can help characterise invading populations in useful ways and can reveal, with greater or lesser precision, the geographical sources of invasions, their timing and how many individuals were involved. Invading mammals may affect the genetics of natives indirectly or directly, and it is important to be able to document this. There is a need to consider both ‘organism invasion’ and ‘gene invasion’. Genetics often provides an unexpected perspective on invasion biology. Examples illustrating all these points are provided through the article.

The rise and fall of species: implications for macroevolutionary and macroecological studies

Knowing the geographic extents of species is crucial for understanding the causes of diversity distributions and modes of speciation and extinction. Species geographic ranges are often viewed as approximately constant in size in geological time, even though climate change studies have shown that historical and modern species geographic distributions are not static. Here, we use an extensive global microfossil database to explore the temporal trajectories of geographic extents over the entire lifespan of marine nannoplankton, diatom, planktic foraminifer and radiolarian species. We show that geographic extents are not static over geological time-scales. Temporal trajectories of species geographic ranges are asymmetric: the rise is quicker than the fall. We propose that once a species has overcome its initial difficulties in geographic establishment, it rises to its peak geographic extent. However, once this peak value is reached, it will also have a maximal number of species to interact with. The negative of these biotic interactions could then cause a gradual geographic decline. We discuss the multiple implications of our findings with reference to macroecological and macroevolutionary studies.

Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group)

Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizardXantusia vigilisspecies complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.

Cryptic diversity in Engaeus Erichson, Geocharax Clark and Gramastacus Riek (Decapoda : Parastacidae) revealed by mitochondrial 16S rDNA sequences

Nucleotide sequence data from the mitochondrial 16S rDNA region were utilised to investigate phylogenetic relationships and species boundaries among Australian freshwater crayfish belonging to the genera Engaeus Erichson, 1846, Geocharax Clark, 1936 and Gramastacus Riek, 1972. Geocharax and Gramastacus were found to be monophyletic genera but one species currently assigned to Engaeus may belong to another genus. Relationships between the three existing genera were not resolved. Analysis of species boundaries within Geocharax suggests that there are an additional two species in this genus, and our analysis of Gramastacus indicates that undescribed populations from central New South Wales may comprise a second species. The data provide at least one instance of a taxon crossing the Great Dividing Range and provide confirmation of previously proposed hypotheses seeking to explain trans-Bass Strait distributions of species.