Phylogeny,paraphyly and ecological adaptation of the colour and pattern in the Anolis roquet complex on Martinique

Martinique is an environmentally heterogeneous island with a complex geological history. It is occupied by a solitary anole, Anolis roquet, showing marked geographical variation in colour and other features. Phylogenetic analysis of a segment (1 kb) of the mitochondrial cytochrome b gene across the Anolis roquet series in the southern Lesser Antilles and at 63 localities of Anolis roquet in Martinique indicate that A. roquet is paraphyletic as A. extremus (Barbados) is nested within the Martinique populations. Moreover, divergent phylogenetic lineages exist within Martinique (max. 10.6% uncorrected pairwise), and these lineages are closely associated with the geological history of this complex island. However, objective quantification of the spectroradiometric analysis of hue by delta analysis, together with analysis of the colour pattern, indicate that they are primarily determined by adaptation to environmental conditions, irrespective of these phylogenetic lineages. There is remarkable convergence in hue and pattern in both extreme xeric (dark chevrons on a dull, generally grey/brown, background), and montane conditions (black reticulation and non-UV white spots on a bright, saturated green background). Moreover, parallel trends occur between Martinique and other Lesser Antillean anoles, which further argues for adaptation (increase in green saturation in montane areas and higher levels of UV on the dewlap of some Atlantic forms). As an exception, there are two specific situations where anoles from different lineages look different. These are (i). in the low-altitude regions of the northwest where the northwestern and central lineages make contact, and (ii). in the far south of the island where the southern and central lineages meet.     

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.     

Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ～18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.     

Dating the arthropod tree based on large-scale transcriptome data

Molecular sequences do not only allow the reconstruction of phylogenetic relationships among species, but also provide information on the approximate divergence times. Whereas the fossil record dates the origin of most multicellular animal phyla during the Cambrian explosion less than 540 million years ago(mya), molecular clock calculations usually suggest much older dates. Here we used a large multiple sequence alignment derived from Expressed Sequence Tags and genomes comprising 129genes (37,476 amino acid positions) and 117 taxa, including 101 arthropods. We obtained consistent divergence time estimates applying relaxed Bayesian clock models with different priors and multiple calibration points. While the influence of substitution rates, missing data, and model priors were negligible, the clock model had significant effect. A log-normal autocorrelated model was selected on basis of cross-validation. We calculated that arthropods emerged ~600 mya. Onychophorans (velvet worms) and euarthropods split ~590 mya, Pancrustacea and Myriochelata ~560 mya, Myriapoda and Chelicerata ~555 mya, and 'Crustacea' and Hexapoda ~510 mya. Endopterygote insects appeared ~390 mya. These dates are considerably younger than most previous molecular clock estimates and in better agreement with the fossil record. Nevertheless, a Precambrian origin of arthropods and other metazoan phyla is still supported. Our results also demonstrate the applicability of large datasets of random nuclear sequences for approximating the timing of multicellular animal evolution.     

A journey on plate tectonics sheds light on European crayfish phylogeography

Crayfish can be used as model organisms in phylogeographic and divergence time studies if reliable calibrations are available. This study presents a comprehensive investigation into the phylogeography of the European stone crayfish (Austropotamobius torrentium) and includes samples from previously unstudied sites. Two mitochondrial markers were used to reveal evolutionary relationships among haplogroups throughout the species’ distributional range and to estimate the divergence time by employing both substitution rates and geological calibration methods. Our haplotype network reconstruction and phylogenetic analyses revealed the existence of a previously unknown haplogroup distributed in Romania's Apuseni Mountains. This haplogroup is closely related to others that are endemic in the Dinarides, despite their vast geographical separation (~600 km). The separation is best explained by the well‐dated tectonic displacement of the Tisza–Dacia microplate, which started in the Miocene (~16 Ma) and possibly carried part of the A. torrentium population to the current location of the Apuseni Mountains. This population may thus have been isolated from the Dinarides for a period of ca. 11 m.y. by marine and lacustrine phases of the Pannonian Basin. The inclusion of this geological event as a calibration point in divergence time analyses challenges currently accepted crayfish evolutionary time frames for the region, constraining the evolution of this area's crayfish to a much earlier date. We discuss why molecular clock calibrations previously employed to date European crayfish species divergences should therefore be reconsidered.     

Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species

Divergence time and substitution rate are seriously confounded in phylogenetic analysis, making it difficult to estimate divergence times when the molecular clock (rate constancy among lineages) is violated. This problem can be alleviated to some extent by analyzing multiple gene loci simultaneously and by using multiple calibration points. While different genes may have different patterns of evolutionary rate change, they share the same divergence times. Indeed, the fact that each gene may violate the molecular clock differently leads to the advantage of simultaneous analysis of multiple loci. Multiple calibration points provide the means for characterizing the local evolutionary rates on the phylogeny. In this paper, we extend previous likelihood models of local molecular clock for estimating species divergence times to accommodate multiple calibration points and multiple genes. Heterogeneity among different genes in evolutionary rate and in substitution process is accounted for by the models. We apply the likelihood models to analyze two mitochondrial protein-coding genes, cytochrome oxidase II and cytochrome b, to estimate divergence times of Malagasy mouse lemurs and related outgroups. The likelihood method is compared with the Bayes method of Thorne et al. (1998, Mol. Biol. Evol. 15:1647-1657), which uses a probabilistic model to describe the change in evolutionary rate over time and uses the Markov chain Monte Carlo procedure to derive the posterior distribution of rates and times. Our likelihood implementation has the drawbacks of failing to accommodate uncertainties in fossil calibrations and of requiring the researcher to classify branches on the tree into different rate groups. Both problems are avoided in the Bayes method. Despite the differences in the two methods, however, data partitions and model assumptions had the greatest impact on date estimation. The three codon positions have very different substitution rates and evolutionary dynamics, and assumptions in the substitution model affect date estimation in both likelihood and Bayes analyses. The results demonstrate that the separate analysis is unreliable, with dates variable among codon positions and between methods, and that the combined analysis is much more reliable. When the three codon positions were analyzed simultaneously under the most realistic models using all available calibration information, the two methods produced similar results. The divergence of the mouse lemurs is dated to be around 7-10 million years ago, indicating a surprisingly early species radiation for such a morphologically uniform group of primates.     

Comparative phylogeography of endemic cyprinids in the south-west Iberian Peninsula: evidence for a new ichthyogeographic area

The comparative phylogeography and evolutionary history of three native cyprinid genera, Squalius (subfamily Leuciscinae), Chondrostoma (subfamily Leuciscinae) and Barbus (subgenus Luciobarbus ; subfamily Cyprininae), were examined focusing mainly in the South-Western region of the Iberian Peninsula, where recently described endemic species are present with considerably restricted distribution areas. In order to accomplish that the variation at the complete cytochrome b gene (1140 bp) was analysed for specimens from the South-Western region, and also for representatives of the three genera from all over the Iberian Peninsula. Data indicate different evolutionary histories, with distinct time periods of colonization between the two cyprinid subfamilies in the Iberian Peninsula. Four new Iberian ichthyogeographic areas are accordingly proposed based on congruent phylogeographic and geological evidences: the South-Western, the South-Eastern, the Atlantic and the Mediterranean. Evidence was provided for the older isolation of the South-Western area in the Miocene during the Endorheic Drainages phase, designating a clearly defined and distinct ichthyogeographic area. A new molecular clock calibration is proposed for the subgenus Luciobarbus .     

The colonization of land by animals: molecular phylogeny and divergence times among arthropods

Background  

The earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma). However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses.     

A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean

In this paper we examine the evolutionary relationships of kestrels from mainland Africa, Indian Ocean islands and related areas. We construct a molecular phylogeny of African kestrels, using approximately 1.0 kb of mitochondrial cytochrome b sequence. Our molecular results support an Old World origin for typical kestrels and an ancient divergence of kestrels into the New World, and indicate a more recent radiation of kestrels from Africa via Madagascar towards Mauritius and the Seychelles. Phylogenetic placement of the Australian kestrel suggests a recent origin from African kestrel stock. We compare evolutionary relationships based on kestrel plumage pattern and morphology to our molecular results for the African and Indian Ocean kestrels, and reveal some consistency with the different island forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. We align these divergence estimates to the geological history of Indian Ocean island formation inferred from potassium-argon dating methods. The arrival of kestrels on Mauritius appears consistent with the cessation of volcanic activity on Mauritius. The estimated time and route of divergence of the Seychelles kestrel from Madagascar may be compatible with the emergence of smaller islands during Pleistocene sea level fluctuations.     

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.     

Genetic Tests for Ecological and Allopatric Speciation in Anoles on an Island Archipelago

From Darwin''s study of the Galapagos and Wallace''s study of Indonesia, islands have played an important role in evolutionary investigations, and radiations within archipelagos are readily interpreted as supporting the conventional view of allopatric speciation. Even during the ongoing paradigm shift towards other modes of speciation, island radiations, such as the Lesser Antillean anoles, are thought to exemplify this process. Geological and molecular phylogenetic evidence show that, in this archipelago, Martinique anoles provide several examples of secondary contact of island species. Four precursor island species, with up to 8 mybp divergence, met when their islands coalesced to form the current island of Martinique. Moreover, adjacent anole populations also show marked adaptation to distinct habitat zonation, allowing both allopatric and ecological speciation to be tested in this system. We take advantage of this opportunity of replicated island coalescence and independent ecological adaptation to carry out an extensive population genetic study of hypervariable neutral nuclear markers to show that even after these very substantial periods of spatial isolation these putative allospecies show less reproductive isolation than conspecific populations in adjacent habitats in all three cases of subsequent island coalescence. The degree of genetic interchange shows that while there is always a significant genetic signature of past allopatry, and this may be quite strong if the selection regime allows, there is no case of complete allopatric speciation, in spite of the strong primae facie case for it. Importantly there is greater genetic isolation across the xeric/rainforest ecotone than is associated with any secondary contact. This rejects the development of reproductive isolation in allopatric divergence, but supports the potential for ecological speciation, even though full speciation has not been achieved in this case. It also explains the paucity of anole species in the Lesser Antilles compared to the Greater Antilles.     

Molecular Clock Calibrations and Metazoan Divergence Dates

It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used. However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid) lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates, some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record. Received: 26 January 1999 / Accepted: 14 April 1999     

Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae)

Hybrid viability decreases with divergence time, a pattern consistent with a so-called speciation clock. However, the actual rate at which this clock ticks is poorly known. Most speciation-clock studies have used genetic divergence as a proxy for time, adopting a molecular clock and often far-distant calibration points to convert genetic distances into age. Because molecular clock assumptions are violated for most genetic datasets and distant calibrations are of questionable utility, the actual rate at which reproductive isolation evolves may be substantially different than current estimates suggest. We provide a robust measure of the tempo at which hybrid viability declines with divergence time in a clade of freshwater fishes (Centrarchidae). This incompatibility clock is distinct from a speciation clock because speciation events in centrarchids appear to be driven largely by prezygotic isolation. Our analyses used divergence times estimated with penalized likelihood applied to a phylogeny derived from seven gene regions and calibrated with six centrarchid fossils. We found that hybrid embryo viability declined at mean rate of 3.13% per million years, slower than in most other taxa investigated to date. Despite measurement error in both molecular estimated ages and hatching success of hybrid crosses, divergence time explained between 73% and 90% of the variation in hybrid viability among nodes. This high correlation is consistent with the gradual accumulation of many genetic incompatibilities of small effect. Hybrid viability declined with the square of time, consistent with an increasing rate of accumulation of incompatibilities between divergent genomes (the snowball effect). However, the quadratic slope is due to a lag phase resulting from heterosis among young species pairs, a phenomenon rarely considered in predictions of hybrid fitness. Finally, we found that reciprocal crosses often show asymmetrical hybrid viabilities. We discuss several alternative explanations for this result including possible deleterious cytonuclear interactions. Speciation-clock studies have been a small cottage industry recently, but there are still novel insights to be gained from analyses of more taxonomic groups. However, between-group comparisons require more careful molecular-clock calibration than has been the norm.     

Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary

The green anole lizard (Anolis carolinensis) is a model organism for behavior and genomics that is native to the southeastern United States. It is currently thought that the ancestors of modern green anoles dispersed to peninsular Florida from Cuba. However, the climatic changes and geological features responsible for the early diversification of A. carolinensis in North America have remained largely unexplored. This is because previous studies (1) differ in their estimates of the divergence times of populations, (2) are based on a single genetic locus or (3) did not test specific hypotheses regarding the geologic and topographic history of Florida. Here we provide a multi-locus study of green anole genetic diversity and find that the Florida peninsula contains a larger number of genetically distinct populations that are more diverse than those on the continental mainland. As a test of the island refugia hypothesis in Pleistocene Florida, we use a coalescent approach to estimate the divergence times of modern green anole lineages. We find that all demographic events occurred during or after the Upper Pliocene and suggest that green anole diversification was driven by population divergence on interglacial island refugia in Florida during the Lower Pleistocene, while the region was often separated from continental North America. When Florida reconnected to the mainland, two separate dispersal events led to the expansion of green anole populations across the Atlantic Seaboard and Gulf Coastal Plain.     

The Assembly of an Island Fauna by Natural Invasion: Sources and Temporal Patterns in the Avian Colonization of Barbados

By virtue of their isolation and depauperate faunas, oceanic islands offer unique opportunities to characterize the historical development of ecological communities derived from both natural and anthropogenic invasions. Barbados, an outlying island in the Lesser Antilles, was formed approximately 700,000 YBP by tectonic uplift and was then colonized by birds via natural invasion from the much older volcanic islands in the main Lesser Antillean arc. We investigated the timing and sources of the avian invasion of Barbados by determining levels of mitochondrial DNA (mtDNA) divergence between populations of eight bird species from Barbados and those on the nearby putative source islands of St. Lucia and St. Vincent. Although all Barbados populations appeared to be young relative to the geological age of the island, we found differences among species in their inferred times of colonization and we identified at least two sources of immigrants to Barbados. In contrast to these historical differences across species and populations, our characterization of the mitochondrial genotypes of 231 individual birds suggests that each island population represents the descendants of a single founding maternal lineage. Considered in concert, the results of this molecular survey indicate that the Barbados bird community is composed of species with different invasion histories, which in turn suggests that the island's community composition has changed repeatedly over its 700,000 year history.     

Hominid and gelada baboon evolution: Agreement between molecular and fossil time scales

The time of origin of the hominid lineage has long been debated. Macromolecular studies have consistently shown genetic distances between living humans and African apes to be quite small. The molecular clock hypothesis proposes that the time of separation of these lineages is relatively recent (in the range of 4–8 million years ago) and not 15 million years or more ago as usually suggested. Three independent molecular comparisons yield a mean estimate of 4.6 million years for the hominid-African pongid divergence. The relationship of Theropithecusand Papiois a parallel case within Primates of two taxa which are quite similar at the molecular level, but which are usually thought to have separated relatively long ago. The two cases of seeming discordance between different lines of evidence are analogous. Each involves a speciation event which eventually resulted in one substantially derived lineage and one or more relatively unchanged lineages. In each case, claims of the antiquity of the divergence event extend to at least twice the age of the first certain appearance of the more derived lineage in the fossil record. Finally, in each case, the molecular clock model suggests a range of possible divergence times that overlaps with the first appearances of undoubted hominids and Theropithecusin the fossil record. This test involving paleontological evidence supports the molecular clock hypothesis.     

Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1

A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around approximately 245 Mya, is estimated at only approximately 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split ( approximately 210 Mya) matches the fossil record; the squamate radiation ( approximately 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of approximately 220 and approximately 165 Myo (million-year-old) fossils as acrodont iguanians and approximately 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (< or = 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.     

Body mass‐corrected molecular rate for bird mitochondrial DNA

Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.     

AND IF ENGLER WAS NOT COMPLETELY WRONG? EVIDENCE FOR MULTIPLE EVOLUTIONARY ORIGINS IN THE MOSS FLORA OF MACARONESIA

The Macaronesian endemic flora has traditionally been interpreted as a relict of a subtropical element that spanned across Europe in the Tertiary. This hypothesis is revisited in the moss subfamily Helicodontioideae based on molecular divergence estimates derived from two independent calibration techniques either employing fossil evidence or using an Monte Carlo Markov Chain (MCMC) to sample absolute rates of nucleotide substitution from a prior distribution encompassing a wide range of rates documented across land plants. Both analyses suggest that the monotypic Madeiran endemic genus Hedenasiastrum diverged of other Helicodontioideae about 40 million years, that is, well before Macaronesian archipelagos actually emerged, in agreement with the relict hypothesis. Hedenasiastrum is characterized by a plesiomorphic morphology, which is suggestive of a complete morphological stasis over 40 million years. Macaronesian endemic Rhynchostegiella species, whose polyphyletic origin involves multiple colonization events, evolved much more recently, and yet accumulated many more morphological novelties than H. percurrens. The Macaronesian moss flora thus appears as a complex mix of ancient relicts and more recently dispersed, fast‐evolving taxa.     

Mitochondrial DNA phylogeography of Semisulcospira libertina (Gastropoda: Cerithioidea: Pleuroceridae): implications the history of landform changes in Taiwan

The mitochondrial DNA cytochrome c oxidase subunit I sequences from 95 specimens of Semisulcospira libertina in Taiwan were identified as two major phylogroups, exhibiting a southern and northern distribution, north of Formosa Bank and south of Miaoli Plateau. The genetic distance between these two phylogroups was 12.20 %, and the distances within-phylogroups were 4.97 and 5.56 %. According to a molecular clock of 1.56 % per lineage per million years, the divergence time between these two major phylogroups was estimated at 4.94 million years ago (mya), with the two phylogroups forming at 3.64 and 3.75 mya, respectively. Moreover, the geological events have suggested that Taiwan Island emerged above sea level at 4–5 mya, and became its present shape at 2 mya. These results suggested that these two phylogroups might originate from two independent ancestral populations or divergent before colonizing Taiwan. Within South phylogroup, the initial colonization was hypothesized to be in Kaoping River (WT), followed by its northward. The high divergence between south- and north of WT River was influenced by the formation of the Kaoping foreland basins. Within North phylogroup, the colonization was from central sub-region through paleo-Miaoli Plateau to northern and northeastern sub-regions. This study showed that the landform changes might have shaped the genetic structure of S. libertina in concert. Apparently, two cryptic species or five different genetic stocks of S. libertina could be identified; these results are useful for the evaluation and conservation of S. libertina in Taiwan.