Crown Age Research Articles

Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context.

Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.

The delayed and geographically heterogeneous diversification of flowering plant families.

The Early Cretaceous (145-100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66-56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37-56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution.

Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae)

Intergeneric relationships of the Beilschmiedia group (Lauraceae) remain unresolved, hindering our understanding of their classification and evolutionary diversification. To remedy this, we sequenced and assembled complete plastid genomes (plastomes) from 25 species representing five genera spanning most major clades of Beilschmiedia and close relatives. Our inferred phylogeny is robust and includes two major clades. The first includes a monophyletic Endiandra nested within a paraphyletic Australasian Beilschmiedia group. The second includes (i) a subclade of African Beilschmiedia plus Malagasy Potameia, (ii) a subclade of Asian species including Syndiclis and Sinopora, (iii) the lone Neotropical species B. immersinervis, (iv) a subclade of core Asian Beilschmiedia, sister to the Neotropical species B. brenesii, and v) two Asian species including B. turbinata and B. glauca. The rampant non-monophyly of Beilschmiedia we identify necessitates a major taxonomic realignment of the genus, including but not limited to the mergers of Brassiodendron and Sinopora into the genera Endiandra and Syndiclis, respectively. Along these lines, the high degree of continental, clade-wide endemism we identify suggests that geographical distribution may be a good proxy for delineating taxa within this group. Our molecular divergence time estimates indicate that stem Beilschmiedia group members date to the Early Eocene (~50 Ma); their crown age dates to the Eocene–Oligocene boundary (~34 Ma). These findings contradict older estimates of the group and support mounting evidence that the origin and diversification of many pantropical angiosperm clades are not easily attributed to strict western Gondwanan vicariance. Finally, our study highlights the phylogenetic utility of plastomes in Lauraceace, and lays a solid foundation for future phylogenomic and biogeographic investigations within the family.

Phylogenomic Study of Monechma Reveals Two Divergent Plant Lineages of Ecological Importance in the African Savanna and Succulent Biomes

Monechma Hochst. s.l. (Acanthaceae) is a diverse and ecologically important plant group in sub-Saharan Africa, well represented in the fire-prone savanna biome and with a striking radiation into the non-fire-prone succulent biome in the Namib Desert. We used RADseq to reconstruct evolutionary relationships within Monechma s.l. and found it to be non-monophyletic and composed of two distinct clades: Group I comprises eight species resolved within the Harnieria clade, whilst Group II comprises 35 species related to the Diclipterinae clade. Our analyses suggest the common ancestors of both clades of Monechma occupied savannas, but both of these radiations (~13 mya crown ages) pre-date the currently accepted origin of the savanna biome in Africa, 5–10 mya. Diversification in the succulent biome of the Namib Desert is dated as beginning only ~1.9 mya. Inflorescence and seed morphology are found to distinguish Groups I and II and related taxa in the Justicioid lineage. Monechma Group II is morphologically diverse, with variation in some traits related to ecological diversification including plant habit. The present work enables future research on these important lineages and provides evidence towards understanding the biogeographical history of continental Africa.

Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)

Abstract Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to infer these relationships. We constructed both concatenation and coalescent-based estimates of phylogeny from this dataset using matrices of varying levels of completeness, and we generated a time-scaled ultrametric tree using a recently published fossil-based external calibration. We found uniformly strong support for a monophyletic subfamily Euphoniinae and genus Chlorophonia, but a paraphyletic Euphonia across UCEs and mitochondrial genomes. Otherwise, our inferred relationships were largely concordant with previous studies. Our time-tree indicated a stem divergence time of 13.8 million years ago for this lineage, followed by a relatively young crown age of only 7.1 myr. Reconstructions of biogeographic history based on this tree suggest a South American origin for crown Euphoniinae, possibly resulting from a transoceanic dispersal event from the Eastern Hemisphere, followed by 2 dispersal events into the Caribbean and as many as 6 invasions of North America coinciding with recent estimates of the age at which the Isthmus of Panama had completely formed. We recommend splitting Euphonia and resurrecting the genus Cyanophonia for the 3 blue-hooded species more closely related to Chlorophonia. Based on our results, we suspect that there is undescribed species-level diversity in at least one, possibly many, widespread and phenotypically diverse species.

Elucidation of the life cycle of the endophytic genus Muscodor and its transfer to Induratia in Induratiaceae fam. nov., based on a polyphasic taxonomic approach

Molecular phylogenetic studies of cultures derived from some specimens of plant-inhabiting Sordariomycetes using ITS, LSU, rpb2 and tub2 DNA sequence data revealed close affinities to strains of Muscodor. The taxonomy of this biotechnologically important genus, which exclusively consists of endophytes with sterile mycelia that produce antibiotic volatile secondary metabolites, was based on a rather tentative taxonomic concept. Even though it was accommodated in Xylariaceae, its phylogenetic position had so far remained obscure. Our phylogeny shows that Muscodor species have affinities to the xylarialean genera Emarcea and Induratia, which is corroborated by the fact that their sexual states produce characteristic apiospores. These data allow for the integration of Muscodor in Induratia, i.e. the genus that was historically described first. The multi-locus phylogenetic tree clearly revealed that a clade comprising Emarcea and Induratia forms a monophylum separate from representatives of Xylariaceae, for which we propose the new family Induratiaceae. Divergence time estimations revealed that Induratiaceae has been diverged from the Xylariaceae + Clypeosphaeriaceae clade at 93 (69–119) million years ago (Mya) with the crown age of 61 (39–85) Mya during the Cretaceous period. The ascospore-derived cultures were studied for the production of volatile metabolites, using both, dual cultures for assessment of antimicrobial effects and extensive analyses using gas chromatography coupled with mass spectrometry (GC–MS). The antimicrobial effects observed were significant, but not as strong as in the case of the previous reports on Muscodor species. The GC–MS results give rise to some doubt on the validity of the previous identification of certain volatiles. Many peaks in the GC–MS chromatograms could not be safely identified by database searches and may represent new natural products. The isolation of these compounds by preparative chromatography and their subsequent characterisation by nuclear magnetic resonance (NMR) spectroscopy or total synthesis will allow for a more concise identification of these volatiles, and they should also be checked for their individual contribution to the observed antibiotic effects. This will be an important prerequisite for the development of biocontrol strains.

First Age-Estimation Model for Dracaena ombet and Dracaena draco subsp. caboverdeana

Research Highlights: The first model for crown age estimation was developed for Dracaena ombet Heuglin ex Kotschy and Peyr. and D. draco subsp. caboverdeana Marrero Rodr. and R. Almeida. Background and Objectives: Dracaena species are monocotyledon trees without annual tree rings. Most arborescent dragon tree species are endangered; thus, it is important to determine the age structures of these populations for proper conservation management strategies, and for modelling of population trends. For these reasons, it is necessary to develop a methodology of crown age estimation. Materials and Methods: Field data were collected in the Desa’a Forest (Ethiopia) and in Santo Antão (Cape Verde Islands). Trees within each age class, as expressed by the number of branch orders, were measured. The diameter at breast height, tree height, stem height, number of branch orders, number of all leaf rosettes and number of flowering leaf rosettes within the crown were recorded for each sampled tree. The flowering probabilities were counted as input data for the model used. Results: The duration of the interval between flowering events was 5.23 years for D. ombet and 4.94 years for D. draco subsp. caboverdeana. The crown of the oldest tree of D. ombet with 18 branch orders was estimated to be 94.2 years old, and the crown of the oldest tree of D. draco subsp. caboverdeana with 22 branch orders was estimated to be 108.6 years old.

Phylogeny and divergence estimates for the gasteruptiid wasps (Hymenoptera : Evanioidea) reveals a correlation with hosts

The Gasteruptiidae are an easily recognised family of wasps whose larvae are considered predator-inquilines in the nests of solitary bees and wasps. There has been minimal molecular research on the family and as a result little understanding of the evolutionary relationships within the group. We present the first molecular phylogeny focused on Gasteruptiidae, generated using three molecular fragments (mitochondrial C01 and nuclear markers EF1-α and 28s) and estimate the divergence times of Evanioidea based on three secondary calibration points. The analyses included 142 specimens of Gasteruptiidae and 5 outgroup taxa from Aulacidae and Evaniidae. The monophyly of the Gasteruptiidae and its subfamilies Gasteruptiinae (Gasteruption) and Hyptiogastrinae (Hyptiogaster and Pseudofoenus) are confirmed. Our results indicate that Evanioidea diverged during the late Jurassic at 151.3 (171.99–136.15)Ma with Evaniidae during the early Cretaceous at 137.33 (140.86–133.67)Ma, and Gasteruptiidae during the Palaeocene at 60.23 (83.78–40.02)Ma. The crown age of Hyptiogastrinae was estimated to be during the mid-Eocene 40.72 (60.9–22.57)Ma and for Gasteruption during the early Eocene at 47.46 (64.7–31.75)Ma, which corresponded to their host divergence ages. We anticipate that more extensive taxon sampling combined with the use of phylogenomic data will help resolve low support within the Gasteruption clade.

Species delimitation and evolutionary relationships among Phoebis New World sulphur butterflies (Lepidoptera, Pieridae, Coliadinae)

ABSTRACTThe most accepted taxonomic treatment of the New World sulphurs of the genus Phoebis Hübner, [1819] recognizes 16 species including those in the current synonyms Aphrissa and Rhabdodryas. This total conflicts with the results of several recent pierid DNA barcode studies across the Neotropics. We used a five‐locus dataset to carry out species delimitation analyses using the coalescence‐based method implemented in bpp software. After testing the resulting species hypotheses using marginal likelihood estimates, we inferred their phylogenetic relationships and performed an ancestral range reconstruction with biogeobears. Our analyses recovered two different hypotheses, 26 and 24 species, that scored the highest marginal likelihood estimate. Differences between these two hypotheses, when reconciled with barcode clusters and morphology, indicated that 24 is the most likely number of species. Phoebis neocypris stat. rev., Phoebis rurina stat. rev., Phoebis virgo stat. rev., Phoebis marcellina stat. rev., Phoebis thalestris stat. rev., and Phoebis rorata stat. rev. are raised to the species rank. We dated the crown age of Phoebis to the mid‐Miocene, with the islands of the Greater Antilles as the most probable ancestral range. Three main clades of Phoebis diverged early in the evolutionary history of the genus, but most extant species‐level diversity arose after the Pliocene–Pleistocene boundary. Our analyses recovered alternate range expansions and contractions, and dispersal from the islands to the continent and back, in the three main clades. Both sympatric and allopatric speciation seem to have shaped the current species richness.

Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi)

Abstract Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.

Phylogenetic affinity of an enigmatic Rubiaceae from the Seychelles revealing a recent biogeographic link with Central Africa: gen. nov. Seychellea and trib. nov. Seychelleeae

The granitic islands of the Seychelles harbor about 268 native angiosperm species, with 28% being endemics there. The Seychelles biota contains a mix of ancient taxa with Gondwanan origins and young taxa that arrived there via dispersals. We investigate the phylogenetic position of an enigmatic, critically endangered, Seychellean endemic of the coffee family (Rubiaceae), Psathura/Psychotria sechellarum, and assess whether its presence on the granitic islands of the Seychelles is the result of vicariance or long-distance dispersal. Phylogenetic relationships of the family were reconstructed based on the Bayesian and maximum-likelihood phylogenetic analyses of sequence data from five plastid markers of 107 terminals. Divergence times were estimated using a Bayesian-based method. Psathura/Psychotria sechellarum is distantly related to Psychotria s.l. (including Psathura), and is strongly supported as sister to the Central African genus Colletoecema. Their striking morphological differences, coupled with their geographic separation and genetic distinctness, support the recognition of the new genus Seychellea and new tribe Seychelleeae to accommodate the Seychellean species. The Colletoecema-Seychellea clade constitutes an early-divergent lineage in the subfamily Rubioideae, with an old stem and a young crown ages estimated to be in the Late Cretaceous and late Oligocene-early Pliocene, respectively. Colletoecema diverged from Seychellea in the late Oligocene-early Pliocene and their respective crown ages are inferred to be late Miocene-middle Pleistocene and Pleistocene, respectively. The ancestor of the two genera was likely present in Africa, and reached the Seychelles via avian dispersal. Unlike Colletoecema with three species, Seychellea is monospecific, with very few individuals left in the wild. The species should be a top candidate for conservation priority, as its extinction would cause loss of genetic diversity of this entire lineage.

The assembly of the Cape flora is consistent with an edaphic rather than climatic filter

The Cape flora is compositionally biased, being dominated by a few fynbos clades (such as Iridaceae, Ericaceae, Proteaceae and Restionaceae) that make up major part of the distinct heathland vegetation in the Cape Floristic Region. Uncertainty exists concerning what excluded the subtropical to tropical palm-dominated woodland/forest vegetation that was the dominant component in the CFR in the Paleocene and allowed the fynbos clades, which are largely derived from outside Africa, to establish and radiate. Two filters have been proposed. The first postulates that the establishment of the Mediterranean climate driven by the late Miocene initiation of the cold-water Benguela Upwelling System (BUS) eliminated the African lineages and allowed the establishment and radiation of sclerophyllous plant clades (“the Mediterranean climate model”, MCM). Alternatively, the “oligotrophic soils model” (OSM) postulates that the oligotrophic soils, gradually exhumed by post-Gondwanan Late Cretaceous – early Cenozoic erosion, acted as a filter excluding the African lineages. In this study, we re-calibrate the fynbos clade Phylica (Rhamnaceae), the genus initially used to test the MCM, using new fossil data to test if the crown age precedes the Late Miocene. Our results indicate that we cannot significantly reject a crown age of Phylica consistent with the MCM. We compare the MCM and OSM model for the Cape fynbos flora by compiling the crown ages of 22 fynbos clades. We show that crown ages are not clustered in time around the initiation of the BUS but, are dispersed throughout the Cenozoic. This suggests that oligotrophic soils, rather than summer drought, acted as a filter. Consequently, we argue that the fynbos clades radiated separately in expanding edaphically controlled heathland patches in the Cape mountains as sandstone exhumation after the Gondwanan break-up progressed.

Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression.

Hawaiian Melicope are one of the major adaptive radiations of the Hawaiian Islands comprising 54 endemic species. The lineage is monophyletic with an estimated crown age predating the rise of the current high islands. Phylogenetic inference based on Sanger sequencing has not been sufficient to resolve species or deeper level relationships. Here, we apply restriction site-associated DNA sequencing (RAD-seq) to the lineage to infer phylogenetic relationships. We employ Quartet Sampling to assess information content and statistical support, and to quantify discordance as well as partitioned ABBA-BABA tests to uncover evidence of introgression. Our new results drastically improved resolution of relationships within Hawaiian Melicope. The lineage is divided into five fully supported main clades, two of which correspond to morphologically circumscribed infrageneric groups. We provide evidence for both ancestral and current hybridization events. We confirm the necessity for a taxonomic revision of the Melicope section Pelea, as well as a re-evaluation of several species complexes by combining genomic and morphological data.

Phylogeny and biogeography of the cleptoparasitic bee genus Epeolus (Hymenoptera: Apidae) and cophylogenetic analysis with its host bee genus Colletes (Hymenoptera: Colletidae)

The bee genus Epeolus Latreille (Hymenoptera: Apidae) consists of 109 species, which are known to be exclusively cleptoparasites of polyester (or cellophane) bees of the genus Colletes Latreille (Hymenoptera: Colletidae). Both genera have a nearly cosmopolitan distribution and are represented on all continents except Antarctica and Australia. We present the most comprehensive phylogeny for Epeolus to date, based on combined molecular and morphological data. In total, 59 ingroup taxa (species of Epeolus) and 7 outgroup taxa (other Epeolini) were scored for 99 morphological characters, and sequence data were obtained for seven genes (one mitochondrial and six nuclear, 5399 bp in total). Epeolus was found to be monophyletic, with a crown age estimated to be 25.0–13.4 Ma (95% HPD) and its origins traced to the Nearctic region. Epeolus was found to contain six major clades, five of which were well supported. The evolutionary history of Epeolus is explored in the context of earth history events and the evolutionary history of its host genus Colletes, for which a molecular phylogeny was constructed based on the same seven genes. A comparison of Epeolus and Colletes phylogenies limited to taxa for which there is evidence of an association suggests there was some cospeciation. However, more cladogenetic events in Epeolus were linked to instances of dispersal/vicariance. It is not yet clear the extent to which allopatric speciation contributed to diversification in Colletes, but the genus’ success in having colonized and diversified across much of the globe made it possible for Epeolus to do the same.

Colonization time on island settings: lessons from the Hawaiian and Canary Island floras

Abstract Molecular dating offers a tool for inferring the time of divergence between two lineages. In this study, we discuss how dated molecular reconstructions are informative of two different, albeit often intermingled, time estimates with regard to a fundamental process in island biogeography: the time of island colonization (TIC). We illustrate how stem age estimates provide information on the divergence between the extant island lineage and their closest relatives (i.e. the onset of lineage differentiation). Such estimates, however, are typically poor TIC predictors, as they are strongly affected by spatial and temporal uncertainty, particularly in cases of deep stem ages. Crown ages of endemic island lineages, in contrast, provide information on the temporal onset of island in situ diversification, and may represent a better proxy for TIC when the associated uncertainty is taken into account. Thus, the geographic and temporal distance separating the island and mainland lineages in phylogenetic/phylogeographic reconstructions are key factors for determining the reliability of these two estimates as proxies of TIC. We show how divergence times can be used to investigate the biogeographic patterns of two well-studied oceanic archipelagos: Hawaii and the Canary Islands. A compilation of molecular age estimates for nearly one-third of the endemic plant lineages in each archipelago reveals that Canarian plant lineages exhibit significantly younger mean crown ages (2.1 ± 2.4 Myr) than Hawaiian lineages (3.5 ± 2.9 Myr), despite island substrates being much older in the Canarian archipelago. We postulate that this pattern suggests: (1) a more important role of submerged islands during plant colonization in Hawaii, and (2) higher taxon turnover in the Canaries, mediated by relatively young (Mediterranean) lineages, and probably facilitated by the combination of the high incidence of extinction for the last 5 Myr and the close proximity of mainland source areas as compared to Hawaii.

Historical biogeography of a Brazilian lineage of Tillandsioideae (subtribe Vrieseinae, Bromeliaceae): the Paranaean Sea hypothesized as the main vicariant event

Abstract Subtribe Vrieseinae comprise four genera, Alcantarea, Stigmatodon, Vriesea s.s. and Waltillia, encompassing c. 20% of species in Tillandsioideae (Bromeliaceae), almost all of which are exclusive to Brazil. Here, we explore the biogeographic history of Vrieseinae, sampling 21 of the 22 genera of Tillandsioideae (130 terminals) and three DNA sequence markers (two plastid: rps16-trnK and matK; one nuclear: PHYC). We inferred a dated phylogeny and the ancestral areas of this lineage through RASP (reconstruct ancestral state in phylogeny) analyses. Vrieseinae were recovered as monophyletic, but tribe Vrieseeae (subtribe Vrieseinae + subtribe Cipuropsidinae) were not. A vicariant event between the Andes and Brazilian Shield probably occurred c. 10 Mya, when two clades, Cipuropsidineae + Tillandsieae and Vrieseineae, diverged. The Atlantic Forest plus the Chacoan region is recognized as the ancestral area for Vrieseinae. The results confirmed the recent origin of genera of Vrieseinae, with estimated crown ages in the Pliocene (5.3–2.6 Mya). We propose that the Paranaean Sea influenced the divergence of the main clades; Pleistocene events were probably responsible for the diversification of the most recent clades. This study sheds light on the biogeographic history of a key group of Neotropical plants, providing a new hypothesis for the evolution of bromeliads.

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

AbstractMice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

Cenozoic formation and colonisation history of the New Zealand vascular flora based on molecular clock dating of the plastid rbcL gene

ABSTRACTA colonisation history for 411 extant genera and 477 lineages of the vascular flora of New Zealand was constructed using the plastid rbcL gene. Molecular clock crown ages suggest that the Eocene-Oligocene transition extinction at 33.9 Ma was critical to the development of the extant flora as few lineages, mostly ferns and conifers, predate this event. Based on crown dates, almost all extant angiosperm lineages have established after the Eocene-Oligocene transition extinction. The Oligocene marine transgression had little discernible impact on the formation of the extant flora, as at the culmination of the inundation (22.0–25.0 Ma) fifty extant lineages of vascular plant were present and another eight lineages originated during this time. The majority of extant species (89%) originated after the end of the Miocene Thermal Optimum at about 15.0 Ma. Nearly 50% of the extant species have evolved during mountain uplift and glaciation of the late Pliocene-Pleistocene (0–4.99 Ma). Therefore, despite a residual contribution from the Eocene, Oligocene and early to mid Miocene periods, the New Zealand vascular flora essentially originated in the late Miocene and after.

Body size evolution in palaeognath birds is consistent with Neogene cooling-linked gigantism

Palaeognathae is an extant clade of birds with body masses ranging over several orders of magnitude of kilograms, including the largest-yet described terrestrial avian species. Most studies have suggested flight loss and increasing body size began early in its evolutionary history, prior to the divergence of the major extant lineages. However, recent phylogenetic work suggests body size increases occurred more recently and independently within many extant lineages. Here, we use linear regression equations to estimate the masses of extinct taxa from both the crown and stem of Palaeognathae to test these hypotheses. We allocate fragmentary specimens to discrete body mass categories to accommodate additional species for which more precise body mass estimation is not possible. The first fossil evidence for an increase in maximum palaeognath body size, from approximately that of a rhea (20 kg) or smaller to ostrich size (100 kg), is Miocene in age (approximately 20 Ma). The heaviest taxa, those exceeding 120 kg, all occur within the last 9 million years. Molecular divergence dating estimates for the crown ages of palaeognath subclades pre-date the oldest preserved material, often significantly; however, plotting the lightest member of each clade at the estimated crown ages does not change the observed pattern. These results may be affected by the predictive model used to estimate the mass of extinct taxa, but the observed trends in body mass do not change when four models from different studies are used. Both island-dwelling and continental clades show broad temporal congruence in the timing of their estimated gain of large body sizes, meaning geographical restriction on islands does not alone explain the observed trend. We suggest large and giant Palaeognathae body sizes may be more closely linked to global cooling which creates selective pressures on body size for thermoregulation, as well as causing landscape changes which alters dietary and locomotory requirements. Global cooling has received extensive attention as a driver of mammalian body size extremes but has been relatively little discussed with respect to birds.

A multigene timescale and diversification dynamics of Ciliophora evolution

Ciliophora is one of the most diverse lineages of unicellular eukaryotes. Nevertheless, a robust timescale including all main lineages and employing properly identified ciliate fossils as primary calibrations is lacking. Here, we inferred a time-calibrated multigene phylogeny of Ciliophora evolution, and we used this timetree to investigate the rates and patterns of lineage diversification through time. We implemented a two-step analytical approach that favored both gene and taxon sampling, reducing the uncertainty of time estimates and yielding narrower credibility intervals on the ribosomal-derived chronogram. We estimate the origin of Ciliophora at 1143 Ma, which is substantially younger than previously proposed ages, and the huge diversity explosion occurred during the Paleozoic. Among the current groups recognized as classes, Spirotrichea diverged earlier, its origin was dated at ca. 850 Ma, and Protocruziea was the younger class, with crown age estimated at 56 Ma. Macroevolutionary analysis detected a significant rate shift in diversification dynamics in the spirotrichean clade Hypotrichia + Oligotrichia + Choreotrichia, which had accelerated speciation rate ca. 570 Ma, during the Ediacaran-Cambrian transition. For all crown lineages investigated, speciation rates declined through time, whereas extinction rates remained low and relatively constant throughout the evolutionary history of ciliates.