Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (～12 Ma), with most tribes diversifying throughout the Late Miocene (6.9–9.4 Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.     

Phylogenetic relationships and evolutionary history of the reef fish family Labridae

The family Labridae (including scarines and odacines) contains 82 genera and about 600 species of fishes that inhabit coastal and continental shelf waters in tropical and temperate oceans throughout the world. The Labridae (the wrasses) is the fifth largest fish family and second largest marine fish family, and is one of the most morphologically and ecologically diversified families of fishes in size, shape, and color. Labrid phylogeny is a long-standing problem in ichthyology that is part of the larger question of relationships within the suborder Labroidei. A phylogenetic analysis of labrids was conducted to investigate relationships among the six classical tribes of wrasses, the affinities of the wrasses to the parrotfishes (scarines), and the broad phylogenetic structure among labrid genera. Four gene fragments were sequenced from 98 fish species, including 84 labrid fishes and 14 outgroup taxa. Taxa were chosen from all major labrid clades and most major global ocean regions where labrid fishes exist, as well as cichlid, pomacentrid, and embiotocid outgroups. From the mitochondrial genome we sequenced portions of 12S rRNA (1000 bp) and 16S rRNA (585 bp), which were aligned by using a secondary structure model. From the nuclear genome, we sequenced part of the protein-coding genes RAG2 (846 bp) and Tmo4C4 (541 bp). Maximum likelihood, maximum parsimony, and Bayesian analyses on the resulting 2972 bp of DNA sequence produced similar topologies that confirm the monophyly of a family Labridae that includes the parrotfishes and butterfishes and strong support for many previously identified taxonomic subgroups. The tribe Hypsigenyini (hogfishes, tuskfishes) is the sister group to the remaining labrids and includes odacines and the chisel-tooth wrasse Pseudodax moluccanus, a species previously considered close to scarines. Cheilines and scarines are sister-groups, closely related to the temperate Labrini, and pseudocheilines and cheilines are split in all phylogenies. The razorfishes (novaculines) and temperate pseudolabrines form successive sister clades to the large crown group radiation of the Julidini. The cleaner wrasses (Labrichthyini) are nested within this radiation and several julidine genera do not appear to be monophyletic (e.g., Coris and Halichoeres). Invasion of temperate water by this predominantly tropical group has occurred multiple times and the reconstruction of biogeography assuming an Indo-Pacific ancestor results in five different lineages invading the Atlantic/Caribbean region. Functional novelties in the feeding apparatus have allowed labrid fishes to occupy nearly every feeding guild in reef environments, and trophic variation is a central axis of diversification in this family.     

Evolution of Strigamia centipedes (Chilopoda): a first molecular assessment of phylogeny and divergence times

We present a first phylogenetic and temporal framework, with biogeographical insights, for the centipedes of the genus Strigamia, which are widespread predators in the forest soils of the Northern Hemisphere and comprise the evo‐devo model species Strigamia maritima. The phylogeny was estimated by different methods of maximum likelihood and Bayesian inference from sequences of two mitochondrial (16S, COI) and two nuclear (18S, 28S) genes, obtained from 16 species from all major areas of the global range of the genus and encompassing most of the overall morphological and ecological diversity. Divergence times were estimated after calibration upon the fossil record of centipedes. We found that major lineages of extant species of Strigamia separated most probably around 60 million years (Ma) ago. The two most diverse lineages diversified during the last 30 Ma and are today segregated geographically, one in Europe and another in Eastern Asia. This latter region hosts a hitherto underestimated richness and anatomical diversity of species, including three still unknown, yet morphologically well distinct species, which are here described as new: Strigamia inthanoni sp. n. from Thailand, Strigamia korsosi sp. n. from the Ryukyu Islands and Strigamia nana sp. n. from Taiwan. The northern European model species S. maritima is more strictly related to the Eastern Asian lineage, from which it most probably separated around 35 Ma ago before the major diversification of the latter.     

Phylogeny and historical biogeography of ancient assassin spiders (Araneae: Archaeidae) in the Australian mesic zone: evidence for Miocene speciation within Tertiary refugia

The rainforests, wet sclerophyll forests and temperate heathlands of the Australian mesic zone are home to a diverse and highly endemic biota, including numerous old endemic lineages restricted to refugial, mesic biomes. A growing number of phylogeographic studies have attempted to explain the origins and diversification of the Australian mesic zone biota, in order to test and better understand the mode and tempo of historical speciation within Australia. Assassin spiders (family Archaeidae) are a lineage of iconic araneomorph spiders, characterised by their antiquity, remarkable morphology and relictual biogeography on the southern continents. The Australian assassin spider fauna is characterised by a high diversity of allopatric species, many of which are restricted to individual mountains or montane systems, and all of which are closely tied to mesic and/or refugial habitats in the east and extreme south-west of mainland Australia. We tested the phylogeny and vicariant biogeography of the Australian Archaeidae (genus Austrarchaea Forster & Platnick), using a multi-locus molecular approach. Fragments from six mitochondrial genes (COI, COII, tRNA-K, tRNA-D, ATP8, ATP6) and one nuclear protein-coding gene (Histone H3) were used to infer phylogenetic relationships and to explore the phylogeographic origins of the diverse Australian fauna. Bayesian analyses of the complete molecular dataset, along with differentially-partitioned Bayesian and parsimony analyses of a smaller concatenated dataset, revealed the presence of three major Australian lineages, each with non-overlapping distributions in north-eastern Queensland, mid-eastern Australia and southern Australia, respectively. Divergence date estimation using mitochondrial data and a rate-calibrated relaxed molecular clock revealed that major lineages diverged in the early Tertiary period, prior to the final rifting of Australia from East Antarctica. Subsequent speciation occurred during the Miocene (23-5.3 million years ago), with tropical and subtropical taxa diverging in the early-mid Miocene, prior to southern and temperate taxa in the mid-late Miocene. Area cladograms reconciled with Bayesian chronograms for all known Archaeidae in southern and south-eastern Australia revealed seven potentially vicariant biogeographic barriers in eastern Queensland, New South Wales and southern Australia, each proposed and discussed in relation to other mesic zone taxa. Five of these barriers were inferred as being of early Miocene age, and implicated in the initial vicariant separation of endemic regional clades. Phylogeographic results for Australian Archaeidae are congruent with a model of sequential allopatric speciation in Tertiary refugia, as driven by the contraction and fragmentation of Australia’s mesic biomes during the Miocene. Assassin spiders clearly offer great potential for further testing historical biogeographic processes in temperate and eastern Australia, and are a useful group for better understanding the biology and biogeography of the Australian mesic zone.     

Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes

Of the 5000 fish species on coral reefs, corals dominate the diet of just 41 species. Most (61%) belong to a single family, the butterflyfishes (Chaetodontidae). We examine the evolutionary origins of chaetodontid corallivory using a new molecular phylogeny incorporating all 11 genera. A 1759‐bp sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast‐growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline.     

A multilocus phylogeny of archiheterodont bivalves (Mollusca,Bivalvia, Archiheterodonta)

The bivalve clade Heterodonta encompasses more than half of the extant bivalve species and is presently considered a derived group of the modern bivalves (Newell 1965 ; Waller 1998 ). Heterodonta is subdivided into two major lineages, the hyperdiverse Euheterodonta and Archiheterodonta. The latter comprises four relatively small extant families: Astartidae, Carditidae, Condylocardiidae and Crassatellidae, whose relationships and internal phylogeny are poorly understood. We assessed the phylogeny of archiheterodont bivalves using a multilocus data set comprised of molecular sequence data from six loci (18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, cytochrome b, internal transcribed spacer 2 and histone H3). Resultant data sets of ~4 Kb of concatenated molecular sequence data were analysed using probabilistic approaches (maximum likelihood and Bayesian inference) and parsimony direct optimization. We recovered strong support for the monophyly of Archiheterodonta, within which Astartidae is the sister group of Crassatellidae, and these two constitute the sister clade of Carditidae, which is paraphyletic with respect to Condylocardiidae. The relationships among the constituent species groups were evaluated in the context of the archiheterodont fossil record through the estimation of divergence times. Diversification times of archiheterodont families were congruent with bounded estimates of origins based on palaeontological data: Archiheterodonta diversified during the Devonian, 373.1 Ma (95% highest posterior density interval [HPD] 325.8–428.2); Crassatelloidea around the Carboniferous, 330.1 Ma (95% HPD 291.0–372.7); Crassatellidae around the Triassic, 224.0 (95% HPD 140.6–320.2); Astartidae around the Permian, 288.2 Ma (95% HPD 269.2–307.3); and Carditoidea around the Jurassic, 178.8 Ma (95% HPD 120.9–228.3).     

Retracing the evolutionary history of Nothofagus in its geo‐climatic context: new developments in the emerging field of phylogeology

Phylogeographic studies have made a significant contribution to the interpretation of genetic lineage distribution in response to climate changes, such as during glaciation events of the Neogene. However, the effects of ancient landscapes associated with global sea level rises, tectonic processes, and climatology driving lineage evolution have been largely overlooked. These effects can be tested in widespread lineages of cold‐tolerant species that have endured cooling, and thus, phylogeographic patterns may reflect large‐scale processes that were not reset by the ice ages. We hereby combine geological evidence from marine sedimentary basins, Andean orogeny, and climatology with molecular dating and statistical phylogeography to infer how geological and climatic processes affected the distribution of lineages in cold‐tolerant Nothofagus species during the Cenozoic. A total of 239 populations along the entire range of all species within the genus Nothofagus (N. antarctica, N. betuloides, N. dombeyi, N. nitida, and N. pumilio) were sampled and analyzed by sequencing three non‐coding regions of the chloroplast. We found 30 chloroplast DNA haplotypes that were geographically structured. Molecular dating calibrated with fossils revealed that ancestral lineages appeared in Eocene/Oligocene, whereas most divergences took place during the Miocene; in turn, Bayesian skyline plots showed that population expansion occurred in the Early Pleistocene (1.5–1 million years ago). Lineage divergence from all wide‐ranging Nothofagus was spatially and temporally concordant with episodic marine transgressions and warmer times in Patagonia during Eocene/Miocene Epochs. Long‐lasting stable raised areas preserved haplotype diversity throughout Patagonia, from where cold‐tolerant taxa expanded their ranges during pre‐Quaternary times. The detailed study of such ancient divergences is novel and allows us to infer the effects of geological processes on distribution patterns of ancient lineages, that is, phylogeology.     

Uplift-driven diversification revealed by the historical biogeography of the cockroach Cryptocercus Scudder (Blattodea: Cryptocercidae) in eastern Asia

Cryptocercus Scudder is a genus of wingless cockroaches, which spend their lives feeding within rotting wood in old-growth montane forests. Their dispersal capability is likely to be limited because they depend on the succession of temperate forests, but their distribution exhibits intercontinental disjunctions. Although the natural history and conservation biology of the North American species of the genus have received much attention, the evolution of the eastern Asian lineages remains enigmatic. To resolve the geographic patterns and evolutionary history of Cryptocercus in eastern Asia, we analysed genetic data of species from China (27 species), Korea (one species) and the Russian Far East (one species). We performed phylogenetic analyses of seven genes to infer the evolutionary relationships among species of Asian Cryptocercus. We then used Bayesian molecular dating to estimate the evolutionary timescale of the genus. Ancestral geographic distributions were reconstructed in rasp using statistical dispersal-vicariance analysis and statistical dispersal-extinction-cladogenesis. Our maximum-likelihood and Bayesian phylogenetic trees supported four major lineages of Cryptocercus, revealing a clear geographical pattern. The divergence of American and Asian lineages was inferred to have occurred 74.8 Ma (95% credibility interval: 51.1–103.8 Ma), with the diversification of Asian taxa beginning at 30.7 Ma (95% credibility interval: 22.9–40.3 Ma). The most recent common ancestor of Asian Cryptocercus taxa was inferred to have had a broad distribution in Asia. The uplift of the Qinghai-Tibet Plateau in the Palaeogene and Neogene, along with climatic oscillations in the Quaternary, probably had substantial effects on the formation of the disjunction pattern in the Cryptocercus lineages found in the Hengduan Mountains and Qin-Daba Mountains of China. We propose that the distribution of Cryptocercus has been strongly influenced by habitat fragmentation and subsequent allopatric speciation.     

Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot

Aim East Africa is one of the most biologically diverse regions, especially in terms of endemism and species richness. Hypotheses put forward to explain this high diversity invoke a role for forest refugia through: (1) accumulation of new species due to radiation within refugial habitats, or (2) retention of older palaeoendemic species in stable refugia. We tested these alternative hypotheses using data for a diverse genus of East African forest chameleons, Kinyongia. Location East Africa. Methods We constructed a dated phylogeny for Kinyongia using one nuclear and two mitochondrial markers. We identified areas of high phylogenetic diversity (PD) and evolutionary diversity (ED), and mapped ancestral areas to ascertain whether lineage diversification could best be explained by vicariance or dispersal. Results Vicariance best explains the present biogeographic patterns, with divergence between three major Kinyongia clades (Albertine Rift, southern Eastern Arc, northern Eastern Arc) in the early Miocene/Oligocene (> 20 Ma). Lineage diversification within these clades pre‐dates the Pliocene (> 6 Ma). These dates are much older than the Plio‐Pleistocene climatic shifts associated with cladogenesis in other East African taxa (e.g. birds), and instead point to a scenario whereby palaeoendemics are retained in refugia, rather than more recent radiations within refugia. Estimates of PD show that diversity was highest in the Uluguru, Nguru and East Usambara Mountains and several lineages (from Mount Kenya, South Pare and the Uluguru Mountains) stand out as being evolutionarily distinct as a result of isolation in forest refugia. PD was lower than expected by chance, suggesting that the phylogenetic signal is influenced by an unusually low number of extant lineages with long branch lengths, which is probably due to the retention of palaeoendemic lineages. Main conclusions The biogeographic patterns associated with Kinyongia are the result of long evolutionary histories in isolation. The phylogeny is dominated by ancient lineages whose origins date back to the early Miocene/Oligocene as a result of continental wide forest fragmentation and contraction due to long term climatic changes in Africa. The maintenance of palaeoendemic lineages in refugia has contributed substantially to the remarkably high biodiversity of East Africa.     

Phylogeny and the colourful history of jewel bugs (Insecta: Hemiptera: Scutelleridae)

Members of the family Scutelleridae (Heteroptera: Pentatomomorpha: Pentatomoidea) are also called shield bugs because of the greatly enlarged scutellum, or jewel bugs because of the brilliant colours of many species. All scutellerids are phytophagous, feeding on various parts of their host plants. Due to lack of obvious synapomorphies and the failure to apply rigorous phylogenetic methods, the higher classification of Scutelleridae has been disputed for more than 150 years. Here we reconstructed a phylogeny of Scutelleridae based on complete sequences of 18S and 28S nuclear rDNAs and all 13 protein‐coding genes of the mitochondrial genome, with the sampled taxa covering all of the currently recognized subfamilies. The monophyly of Scutelleridae was confirmed by the congruence of the results of analyses conducted using Bayesian inference, maximum likelihood and maximum parsimony. The phylogenetic relationships among subfamilies were well resolved for the first time. Furthermore, time‐divergence studies estimated that the time of origin of Scutelleridae was in the Early Cretaceous (142.1–122.8 Ma), after the origin of the angiosperms. The diversification between the extant subfamilies of Scutelleridae and within the subfamilies occurred from the late Palaeocene to the late Miocene, simultaneously with the rise of the major groups of angiosperms and other phytophagous insects.     

Relationships among the basal lineages of Noctuidae (Lepidoptera,Noctuoidea) based on eight gene regions

In this study, we clarify the relationships between the basal lineages in the moth family Noctuidae using DNA sequence data from eight independent gene regions. Data matrices (6.4 kbp) are analysed using parsimony and model‐based methods (maximum likelihood and Bayesian inference). Our results support the family Noctuidae as a monophyletic group in which most subfamilies have hindwing vein M2 reduced or absent. Our phylogenetic hypothesis suggests that in the Noctuidae, the plesiomorphic condition is that in which vein M2 arises about one‐third of the way up the discocellular vein between the origins of M1 and M3, mainly parallel to M3, and is of thickness similar to vein M3. Most Noctuidae lineages possess an apomorphic (derived) condition in which hindwing vein M2 is markedly reduced or totally absent, so that the cubital vein appears to be three‐branched and these lineages are hence referred to as ‘trifine’. However, Noctuidae also include a number of lineages in which vein M2 is unreduced, or only slightly reduced, and these are more problematic for morphological association with the family Noctuidae. Our results also show that the subfamily Acronictinae is not closely related to Pantheinae, but instead shows a closer association with Amphipyrinae. Among the major lineages of Noctuidae, we postulate a general trend, with numerous exceptions, in larval host plants from woody plants in the basal groups towards herb feeding in derived groups. Similarly, the major radiations of monocot‐feeding groups within the family Noctuidae are in the higher trifines. The following taxonomic changes are proposed: Thiacidinae, syn. nov., a junior synonym of Pantheinae, and Dyopsinae, stat. nov., are reinstated as a subfamily.     

Origins of diverse feeding ecologies within Conus, a genus of venomous marine gastropods

Specialized predators on polychaetes, fishes, hemichordates or other molluscs, members of the predominantly tropical gastropod genus Conus diversified rapidly during the Miocene to constitute the most species-rich modern marine genus. We used DNA sequence data from mitochondrial and nuclear loci of 76 Conus species to generate species-level phylogenetic hypotheses for this genus and then mapped known diets onto the phylogenies to elucidate the origins and evolutionary histories of different feeding specializations. The results indicate that dramatically new feeding modes arose only a few times, that the most derived feeding modes likely arose in the Miocene, and that much of the known diversity of Conus that was generated during Miocene radiations has survived to the present.     

Diversification in the Andes: age and origins of South American Heliotropium lineages (Heliotropiaceae, Boraginales)

The uplift of the Andes was a major factor for plant diversification in South America and had significant effects on the climatic patterns at the continental scale. It was crucial for the formation of the arid environments in south-eastern and western South America. However, both the timing of the major stages of the Andean uplift and the onset of aridity in western South America remain controversial. In this paper we examine the hypothesis that the Andean South American groups of Heliotropium originated and diversified in response to Andean orogeny during the late Miocene and a the subsequent development of aridity. To this end, we estimate divergence times and likely biogeographical origins of the major clades in the phylogeny of Heliotropium, using both Bayesian and likelihood methods. Divergence times of all Andean clades in Heliotropium are estimated to be of late Miocene or Pliocene ages. At least three independent Andean diversification events can be recognized within Heliotropium. Timing of the diversification in the Andean lineages Heliotropium sects.Heliothamnus, Cochranea, Heliotrophytum, Hypsogenia, Plagiomeris, Platygyne clearly correspond to a rapid, late Miocene uplift of the Andes and a Pliocene development of arid environments in South America.     

Regional patterns of evolutionary turnover in Neogene coral reefs from the central Indo-West Pacific Ocean

The Indo-Pacific is an area of intense ecological interest, not least because of the region’s rich biodiversity. Important insights into the origins, evolutionary history, and maintenance of Indo-Pacific reef faunas depend upon the analysis of faunal occurrences derived from detailed stratigraphic sections. We investigated Neogene origination and extinction patterns derived from a combination of new coral occurrences and previously published records from the central Indo-West Pacific Ocean (cIWP, Indonesia, Papua New Guinea and Fiji). Two faunal turnover events were observed. In the first, an increase in generic richness of Scleractinia from the cIWP during the middle Miocene (17–14 Ma) coincided with both large-scale sea level fluctuations and the great Mid-Miocene collision event. We raise the hypothesis that Mid-Miocene origination was facilitated by habitat and population fragmentation associated with tectonism and sea level fall. The second, subsequent, turnover event was characterized by an overall lowering of generic diversity throughout the late Miocene and Pliocene (7–3 Ma), and was followed by a pronounced pulse of extinction at the Pliocene–Pleistocene boundary (~2.6 Ma). With the exception of the onset of Pleistocene sea-level cycles and the onset of northern hemisphere glaciation around 2.5 Ma, which might explain increased extinction during this time interval, there are no tectonic, eustatic, climatic or oceanographic events that neatly coincide with this second episode of Neogene coral taxonomic turnover. Our results reveal a total of 62 genera, including synonyms, from the Miocene to the Pleistocene. Neither episode of turnover among coral genera is exactly coincident with turnover in the Atlantic thus regional environmental change is found to drive Neogene reef dynamics.     

Geographic mode of speciation in a mountain specialist Avian family endemic to the Palearctic

Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south‐central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species‐level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene‐Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.     

Cryptic Genetic Diversity Is Paramount in Small-Bodied Amphibians of the Genus Euparkerella (Anura: Craugastoridae) Endemic to the Brazilian Atlantic Forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.     

Ancient origins of Indo-Pacific coral reef fish biodiversity: a case study of the leopard wrasses (Labridae: Macropharyngodon)

Temporal origins of reef fishes in the Indo-Australian Archipelago were examined using wrasses in the genus Macropharyngodon. The genus was selected as it is morphologically and ecologically distinct, with strongly reef-associated species exhibiting discrete distributions across the Indo-Pacific. Phylogenetic relationships were explored using COI, 16S, and 12S rRNA mitochondrial sequences. Monophyly of the genus was supported by congruent Bayesian, maximum likelihood, and maximum parsimony trees. Estimates of lineage ages based on fossil-calibrated reef fish divergences suggest that Macropharyngodon had an extensive evolutionary history starting in the early Miocene. Repeated divergences of Indian Ocean-Pacific Ocean lineages appear to have occurred over at least 19 million years. Regional endemics represent both old and young clades. Our estimates of early Miocene origins, and mid-Miocene to Pliocene diversifications of Macropharyngodon are supported by recent studies of other reef fish genera, and emphasise the importance of pre-Pleistocene events in generating Indo-Pacific coral reef fish biodiversity.     

Multilocus and morphological analysis of south-eastern Iberian Wall lizards (Squamata,Podarcis)

The phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south-east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear markers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in species delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera lineage from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.     

Adaptive radiation in labrid fishes: A central role for functional innovations during 65 My of relentless diversification

Early burst patterns of diversification have become closely linked with concepts of adaptive radiation, reflecting interest in the role of ecological opportunity in modulating diversification. But, this model has not been widely explored on coral reefs, where biodiversity is exceptional, but many lineages have high dispersal capabilities and a pan‐tropical distribution. We analyze adaptive radiation in labrid fishes, arguably the most ecologically dominant and diverse radiation of fishes on coral reefs. We test for time‐dependent speciation, trophic diversification, and origination of 15 functional innovations, and early bursts in a series of functional morphological traits associated with feeding and locomotion. We find no evidence of time‐dependent or early burst evolution. Instead, the pace of speciation, ecological diversification, and trait evolution has been relatively constant. The origination of functional innovations has slowed over time, although few arose early. The labrid radiation seems to have occurred in response to extensive and still increasing ecological opportunity, but within a rich community of antagonists that may have prevented abrupt diversification. Labrid diversification is closely tied to a series of substantial functional innovations that individually broadened ecological diversity, ultimately allowing them to invade virtually every trophic niche held by fishes on coral reefs.