Divergence Time Estimates Research Articles

Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns

Coleoids are the most diverse group of cephalopod mollusks. While their origin is date during the Mesozoic, the diversification pattern is unknown. However, two hypotheses have been proposed. The first suggests an increasing diversification rate after the Cretaceous–Paleogene extinction event (K–Pg) as consequence of empty habitats left by the ammonites and belemnites. The second hypothesis proposes a mid-Cenozoic increase in diversification rate related to distributional changes during ice ages and biotic interactions. To test these hypotheses, we estimated a lineage through time (LTT) and the gamma-statistic along with model-based diversification rates. These analyses were conducted on a dated molecular phylogeny for coleoids that we reconstructed using five molecular markers (cytochrome b, 16S rRNA, cytochrome oxidase I, rhodopsin, and PAX-6). Our divergence time estimation suggests that coleoids originated in the Mesozoic Era (Middle Triassic) and that both main clades (Decapodiformes and Octopodiformes) diverged in the Cretaceous/Jurassic Period. The LTT, gamma statistic, and diversification rates inferred with the Bayesian Analysis of Macro-evolutionary Mixtures (BAMM), indicate an acceleration in diversification rate over time since the origin of coleoids. Additionally, BAMM allowed us to detect abrupt increases in diversification rate before and after the K-Pg boundary. Our results partially support both hypotheses as all analyses indicate that the coleoid diversification rate was increasing during the Cenozoic. However, our results also indicate increasing diversification rates before the K-Pg boundary. We propose that the radiation of coleoids has been shaped by an acceleration in diversification rate over time, including exceptional episodes of abrupt increases before and after the K-Pg boundary.

Phylogeography of cicadas on continental and oceanic islands in the northwestern Pacific region

AbstractAimGenetic differentiation of terrestrial organisms among islands is assumed to be affected by the geological history of the islands, such as the time elapsed since the formation of islands or straits. Cicadas are generally poor dispersers, but some cicada groups have colonised continental and oceanic islands and evolved into endemic species. Here, we focused on a cicada group in the northwestern Pacific region to reveal the association between intra‐ and interspecific genetic differentiation and the geological history of islands for cicadas on continental islands. We also clarified whether colonisation of oceanic islands was achieved by long‐distance dispersal or artificial introduction.LocationJapanese Archipelago, Ogasawara Islands, Ryukyu Archipelago.TaxonCicadas of the genus Meimuna (Hemiptera: Cicadidae).MethodsWe performed phylogenetic analysis, divergence time estimation, and ancestral area reconstruction using two mitochondrial and four nuclear gene sequences and population genetics analyses, including Bayesian skyline plotting using a mitochondrial gene sequence.ResultsMeimuna opalifera in the Japanese Archipelago, which was connected to the continent during the glacial periods, diverged from the continental populations 0.4 million years ago (Ma). In the Ryukyu Archipelago, which became disconnected from the continent earlier, two endemic species Meimuna kuroiwae and M. oshimensis diverged 2.4 Ma; these species showed differences in intraspecific genetic differentiation and range expansion. Furthermore, Meimuna iwasakii colonised the South Ryukyus from Taiwan Island later than 1.4 Ma, whereas M. boninensis, which is endemic to the oceanic Ogasawara Islands, diverged from M. kuroiwae in the Middle Ryukyus 1.04 Ma.Main conclusionsGenetic divergence among Meimuna species was larger on the continental islands that disconnected earlier, as was expected from the geological history of the islands. However, the pattern of intraspecific genetic differentiation differed between species within the same island region, possibly due to their ecological characteristics. In addition, colonisation of oceanic islands was achieved by long‐distance (possibly wind‐borne) dispersal from the continental islands. Thus, the formation of island cicada fauna was affected by islands’ geological history and species’ ecological characteristics, as well as accidental long‐distance dispersal events.

A new molecular phylogeny for the Tanypodinae (Diptera: Chironomidae) places the Australian diversity in a global context

The non-biting midge subfamily Tanypodinae (Diptera: Chironomidae) is species-rich, ecologically diverse, and near-globally distributed. Within the subfamily, aspects of generic and species-level taxonomy remain poorly understood, in particular the validity of assignment of Australian and New Zealand taxa to genera erected for northern hemisphere (Holarctic) fauna. Here, we place the austral diversity within this global context by extensive geographical and taxonomic sampling in concert with a multilocus phylogenetic approach. We incorporated sequence data for mitochondrial COI, and nuclear 28S and CAD, and conducted Bayesian and maximum likelihood phylogenetic inferences and Bayesian divergence time estimation. The resolved phylogeny supported many associations of Australian taxa with their proposed Holarctic congeners, with the exception of Apsectrotanypus Fittkau, and validates several taxa as endemic. Three of four New Zealand sampled taxa had their sister groups in Australia; New Zealand Monopelopia Fittkau was sister to a German congener. This included the first record of Procladius Kieffer from New Zealand. Most nodes connecting austral and Holarctic taxa clustered around the Cretaceous-Tertiary boundary (60–80 mya), whereas New Zealand-Australia nodes were generally slightly younger (53–57 mya). Together, these data contribute substantially to our understanding of the taxonomy, systematics and biogeography of the Australian Tanypodinae and more broadly to knowledge of Australia’s aquatic insect biodiversity.

Sea surface temperature, rather than land mass or geographic distance, may drive genetic differentiation in a species complex of highly dispersive seabirds.

Seabirds, particularly Procellariiformes, are highly mobile organisms with a great capacity for long dispersal, though simultaneously showing high philopatry, two conflicting life‐history traits that may lead to contrasted patterns of genetic population structure. Landmasses were suggested to explain differentiation patterns observed in seabirds, but philopatry, isolation by distance, segregation between breeding and nonbreeding zones, and oceanographic conditions (sea surface temperatures) may also contribute to differentiation patterns. To our knowledge, no study has simultaneously contrasted the multiple factors contributing to the diversification of seabird species, especially in the gray zone of speciation. We conducted a multilocus phylogeographic study on a widespread seabird species complex, the little shearwater complex, showing highly homogeneous morphology, which led to considerable taxonomic debate. We sequenced three mitochondrial and six nuclear markers on all extant populations from the Atlantic (lherminieri) and Indian Oceans (bailloni), that is, five nominal lineages from 13 populations, along with one population from the eastern Pacific Ocean (representing the dichrous lineage). We found sharp differentiation among populations separated by the African continent with both mitochondrial and nuclear markers, while only mitochondrial markers allowed characterizing the five nominal lineages. No differentiation could be detected within these five lineages, questioning the strong level of philopatry showed by these shearwaters. Finally, we propose that Atlantic populations likely originated from the Indian Ocean. Within the Atlantic, a stepping‐stone process accounts for the current distribution. Based on our divergence time estimates, we suggest that the observed pattern of differentiation mostly resulted from historical and current variation in sea surface temperatures.

An integrative approach uncovered variation within Trapelus ruderatus (Olivier, 1804) (Squamata: Agamidae) in Western Asia

The Agamid lizard Trapelus ruderatus has a large distribution in western Asia. There is as yet neither a comprehensive molecular phylogeny nor morphological variation studies on populations of this species. In the present study, we aimed to evaluate the morphology and genetic attributes of this species from populations in Iran, Turkey, Syria, and Iraq. For the morphological examination, 18 characters (nine metric, eight meristic, and one ratio characters) were examined on all specimens. The populations were divided into four Operational Taxonomic Units (OTUs; three in Iran and one in Turkey). The Iraqi population was distinguished as Trapelus persicus by morphological characters. Morphological analyses confirmed that all OTUs could be considered as distinct and that the Turkey population is clearly separated from the Iranian populations. In the genetic component of the project, two mitochondrial (Cytb and ND2) gene fragments were used to reveal phylogenetic relationships among the populations. Molecular phylogenetic reconstruction showed five distinct clades (three in Iran, one in southeastern Turkey, and one in central-southern Turkey–western Syria). Iraqi populations clustered with T. persicus, with high genetic distances from all other populations, as seen using morphological data. Based on the molecular genetic analyses, southeastern Turkey and central-southern Turkey-Syrian populations are clearly distinct (8.4% mean distance) and far from the type population in Iran. This suggests that they should be considered as different taxa. Iranian populations were differentiated into three major groups, the type population in Fars Province and two others in northwest and western Iran. The morphological and molecular genetic results gave a similar output with three Iranian populations having minor divergence, but being clearly separated from the population in Turkey. We suggest each of these groups should be considered as full species. According to divergence time estimation, T. ruderatus firstly diverged at 26.5 mya and subsequently diversified due to the uplifting of the Zagros Mountains and Anatolian Diagonal 15 mya. Subsequent aridification in the Central Iranian Plateau could also have contributed to the divergence of the Fars lineage 9.6 mya.

Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data

The Rough Greensnake, Opheodrys aestivus, is a moderately sized, semi-arboreal snake broadly distributed throughout eastern North America. Although numerous taxa with similar distributions have been shown to comprise multiple species, O. aestivus has not been examined in a detailed phylogeographic context. Here, we use Sanger-sequence data (one mitochondrial, three nuclear loci) for samples from throughout the distribution of O. aestivus to elucidate phylogeographic patterns in this species. We combine this with ddRADseq data for a subset of samples to test patterns on a more genomically comprehensive scale. In both data sets, we find strong support for three deeply divergent clades within O. aestivus: peninsular Florida, central Texas, and a Main clade comprising the rest of the distribution. Estimates of divergence time suggest that the central Texas and Main clades diverged ∼1.3 million years ago (mya), while the peninsular Florida clade diverged from other lineages ∼2.9 mya, and these lineages diverged from the sister taxon, O. vernalis, ∼6.4 mya. The divergence of peninsular Florida or central Texas populations is not unique among squamates, nor is low levels of divergence from the Atlantic coast to eastern Texas, but this combination of patterns is unusual and yields important insight into the biogeography of North American biota. Further, our approach helps illustrate how dense geographic sampling with limited genomic sequencing can be used as a guide for the selection of samples to test phylogeographic patterns comprehensively. We conclude that elevating O. a. carinatus to species status may better describe the diversity of this genus.

Morphological and molecular phylogenetic analyses ofZepedanulus ishikawai(Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

AbstractHarvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestmanZepedanulus ishikawai(Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based onCO1and16SrRNA sequences of mtDNA, the28SrRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals ofZ. ishikawaiwere monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades ofZ. ishikawai.

Historical biogeography of the Gondwanan freshwater genus Boeckella (Crustacea): Timing and modes of speciation in the Southern Hemisphere

AbstractAimWe investigated evolutionary relationships and biogeographical patterns within the genus Boeckella to evaluate (1) whether its current widespread distribution in the Southern Hemisphere is due to recent long‐distance dispersal or long‐term diversification; and (2) the age and origin of sub‐Antarctic and Antarctic Boeckella species, with particular focus on the most widely distributed species: Boeckella poppei.LocationSouth America, sub‐Antarctic islands, maritime Antarctica, continental Antarctica and Australasia.MethodsTo reconstruct phylogenetic patterns of Boeckella, we used molecular sequence data collected from 12 regions and applied Bayesian and Maximum Likelihood analyses using multiple loci. We also estimated divergence times and reconstructed ancestral ranges using two different models of species evolution.ResultsPhylogenetic analyses and divergence time estimates suggested that Boeckella originated on the Gondwanan supercontinent and initially split into two main clades during the late Cretaceous (ca. 80 Ma). The first clade diversified in Australasia, and the second clade is currently distributed in South America, various sub‐Antarctic islands and Antarctica. Dispersal from South America to the Kerguelen and Crozet archipelagos occurred during the Eocene/Oligocene (B. vallentini) and in the late Pliocene (B. brevicaudata), while South Georgia and the maritime Antarctic were likely colonized during the late Pleistocene (B. poppei).Main conclusionsBoeckella has a Gondwanan origin, with further diversifications after the physical separation of the continental landmasses. Extant populations of Boeckella from the Scotia Arc islands and Antarctic Peninsula originated from South America during the Pleistocene, suggesting that original Antarctic Gondwanan lineages did not survive repeated glacial cycles during the Quaternary ice ages. A continuous decline in the species accumulation rate is apparent within the genus as the early Eocene, suggesting that Boeckella diversification may have decreased due to progressive cooling throughout the Cenozoic era.

50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals.

Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice‐associated prey and ice‐free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous‐time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population present prior to the LGM split into two small refugial populations during peak ice extent. Following ice decline, the western refugial population founded colonies at the South Shetlands, South Georgia, and Bouvetøya, while the eastern refugial population founded the colony on Iles Kerguelen. Postglacial population divergence times closely match geological estimates of when these coastal breeding areas became ice free. Given the predictions regarding continued future warming in polar oceans, these responses of Antarctic fur seals to past climate variation suggest it may be worthwhile giving conservation consideration to potential future breeding locations, such as areas further south along the Antarctic Peninsula, in addition to present colony areas.

Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data.

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.

Molecular phylogeny and evolution of Calaphidinae (Hemiptera: Aphididae).

Calaphidinae is the second-largest subfamily in the family Aphididae. Despite their species diversity and some taxonomic controversy, no phylogenetic studies have been conducted on them thus far. Herein, we report the first molecular phylogeny of Calaphidinae and two related lineages, Phyllaphidinae and Saltusaphidinae, based on five genes (3418 bp) for 126 taxa. Maximum parsimony, maximum-likelihood and Bayesian inference phylogenetic analyses were performed on the multilocus dataset. Divergence time estimation, biogeographical reconstruction, ancestral host plant reconstruction and PhyloType analyses were performed to identify evolutionary trends in Calaphidinae. Our phylogenetic results lead to several conclusions: Phyllaphidinae is a sister group to Calaphidinae s.l.; Calaphidinae is paraphyletic with respect to the former "Saltusaphidinae"; the ingroup clade was subdivided into nine newly recognized lineages; and three subtribes of Calaphidinae (Monaphidina, Calaphdina and Panaphidina) and many genera were not recovered as monophyletic. A new classification is proposed with eight tribal divisions that reflect our phylogenetic results, including three new tribes (Pterocallidini trib.n., Pseudochromaphidini trib.n. and Shivaphidini trib.n.) and three new statuses (Saltusaphidini stat.n., Therioaphidini stat.n. and Myzocallidini stat.n.). The ancestral reconstruction results imply that the ingroup taxa's common ancestor originated in the Eastern Palaearctic and might have fed on Fagaceae in the Late Cretaceous. Later, multiple host shifts and an expanding geographical distribution led to the current species diversity of Calaphidinae. Our reconstructions suggest that species diversification cannot solely be explained by speciation via host shifts and that geographical isolation probably also played a key role. Our results provide new insight into the natural classification and history of the host plant associations and biogeography of Calaphidinae s.l.

Stingless bees in Miocene amber of southeastern China (Hymenoptera: Apidae)

Among the many inclusions from the exceptionally rich fossiliferous amber of Zhangpu, China (Middle Miocene: Langhian), stingless bees (Apinae: Meliponini) are particularly common, analogous to the merely slightly older amber sites of Mexico and the Dominican Republic. While there is a large number of workers in Zhangpu amber, only two species are represented. The systematics and morphology of the tribe Meliponini is outlined, including a revision to terms of orientation and direction when discussing surfaces and features of appendages, all in order to better discuss the traits of the fossils as well as place them into a broader context in the global systematics of stingless bees. The two amber species are representative of two Old World genera of Meliponini: Tetragonula Moure and Austroplebeia Moure. While the former is widespread across southern Asia, Malesia, Papuasia, and Australia, the latter is today known only from New Guinea and Australia. Neither genus occurs in the environs of Zhangpu today. Tetragonula (Tetragonula) florilega Engel, new species, is a generally typical species of the subgenus although it intermingles traits otherwise found in two large species groups of non-Australian Tetragonula s.str. The species of Austroplebeia from Zhangpu is sufficiently distinct to place in a new subgenus, Anteplebeina Engel. Austroplebeia (Anteplebeina) fujianica Engel, new species, shares a long list of character states with Austroplebeia s.str., including the presence of yellow maculation on the face, mesoscutum, mesoscutellum, and metepisternum, found only in this clade among Asiatic Meliponini. Nonetheless, the species differs in the length of the malar space and various features of wing venation. Keys are provided to the genera in Zhangpu amber and the subgenera of both genera. The diversity of stingless bees in amber is discussed, as well as the presence of these two fossils in the Middle Miocene of mainland Asia in relation to prior divergence time estimates, phylogenetic relationships, as well as the paleogeography of the region and potential biogeographic hypotheses. The biological association of stingless bees with resins, particularly the collection of dipterocarp resins, is discussed as Zhangpu amber is a Class II resin likely produced by an extinct species of Dipterocarpaceae (Malvales). Also discussed are the ecological preferences of modern Tetragonula and Austroplebeia relative to the reconstructed paleoenvironment of the Zhangpu amber rainforest. Emendations to the classification of Meliponini are appended, with the following new taxa proposed: Atrichotrigona Engel, new subgenus of Axestotrigona Moure; Lispotrigona V.H. Gonzalez & Engel, new subgenus of Nannotrigona Cockerell; Asperplebeia Engel, new genus; Nanoplebeia Engel, new subgenus of Plebeia Schwarz; Aphaneuropsis Engel, Koilotrigona Engel, Necrotrigona Engel, Dichrotrigona Engel, Nostotrigona Engel, Ktinotrofia Engel, all new subgenera of Trigona Jurine; Chapadapis Engel, new subgenus of Schwarziana Moure. The following higher groups are also established: Hypotrigonina Engel, new sutribe; Heterotrigonitae Engel, new infratribe; Trigoniscitae Engel, new infratribe.

Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation.

Understanding how species adapt to extreme environments is an extension of the main goals of evolutionary biology. While alpine plants are an ideal system for investigating the genetic basis of high-altitude adaptation, genomic resources in these species are still limited. In the present study, we generated reference-level transcriptomic data of five Saussurea species through high-throughput sequencing and de novo assembly. Three of them are located in the highland of the Qinghai-Tibet Plateau (QTP), and the other two are close relatives distributed in the lowland. A series of comparative and evolutionary genomics analyses were conducted to explore the genetic signatures of adaptive evolution to high-altitude environments. Estimation of divergence time using single-copy orthologs revealed that Saussurea species diversified during the Miocene, a period with extensive tectonic movement and climatic fluctuation on the QTP. We characterized gene families specific to the alpine species, including genes involved in oxidoreductase activity, pectin catabolic process, lipid transport, and polysaccharide metabolic process, which may play important roles in defense of hypoxia and freezing temperatures of the QTP. Furthermore, in a phylogenetic context with the branch model, we identified hundreds of genes with signatures of positive selection. These genes are involved in DNA repair, membrane transport, response to UV-B and hypoxia, and reproductive processes, as well as some metabolic processes associated with nutrient intake, potentially responsible for Saussurea adaptation to the harsh environments of high altitude. Overall, our study provides valuable genomic resources for alpine species and gained helpful insights into the genomic basis of plants adapting to extreme environments.

Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus.

Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8Gb. Using long- and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome denovo assembly of NWR. The assembly was 1.29Gb in length, highly repetitive (approx. 76.0%) and contained 46421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O.sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30million years ago (26-30MYA), whereas NWR and Z.latifolia diverged from one another approximately 6-8MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z.latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae).

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

The role of Quaternary glaciations in shaping biogeographic patterns in a recently evolved clade of South American epiphytic orchids

AbstractTo contribute to what is known about involvement of vegetation dynamics in Neotropical speciation, we used the Epidendrum latilabre complex, a taxonomically well-defined species group, to investigate past connections between Amazonian (AM) and Atlantic (AF) forests and address the following topics: (1) divergence times between sister species currently distributed in AM and AF; (2) distribution patterns of ancestral species of the E. latilabre complex and (3) potential routes connecting ancestral ranges between AM and AF. We developed a robust phylogenetic estimate for species of the E. latilabre complex by sequencing two nuclear and six plastid loci. Then, we combined divergence time estimation, ancestral range reconstruction and ecological niche modelling. Our biogeographic reconstruction exhibits a complex pattern of connections among tropical forests east of the Andes in South America. The AM and AF species of the E. latilabre complex are intermixed in the results, and climatic shifts during the Pleistocene (Chibanian) are suggested here as a major force promoting speciation. Sister species tend to be ecologically distinct in their climate niche spaces, and vicariance and peripheral isolation are reconstructed as the main drivers of speciation. There is evidence to suggest that the south-east/north-west bridge and the northern/north-eastern coastal route have been occupied by the ancestors of the E. latilabre complex, and alternative routes across the South American dry diagonal were unlikely. Further studies on Neotropical epiphytic taxa are still necessary for understanding the dynamics of historical connections between AM and AF.

Historical biogeography of the Southeast Asian and Malesian tribe Dissochaeteae (Melastomataceae)

AbstractThe region of Tropical Southeast Asia and the Malay Archipelago is a very appealing area for research due to its outstanding biodiversity, being one of the most species‐rich areas in the world with high levels of endemism, and due to its complex geological history. The high number of species in tribe Dissochaeteae (Melastomataceae) and their tendency to narrow endemism make the tribe an ideal group for examining biogeographic patterns. We sampled 58 accessions spread over 42 accepted and two undescribed species of the Dissochaeteae. Two nuclear (ETS, ITS) and four chloroplast regions (ndhF, psbK‐psbL, rbcL, rpl16) were used for divergence time estimation and ancestral area reconstruction. Results from the molecular dating analysis suggest that the diversity of Dissochaeteae in the Southeast Asian region resulted from a South American ancestor in the late Eocene. The ancestor of the Dissochaeteae might have migrated from South America to Southeast Asia via North America and then entered Eurasia over the North Atlantic land bridge during the Eocene. The origin and early diversification of the Dissochaeteae in Southeast Asia dates back to the middle Oligocene, and most of the genera originated during the Miocene. Indochina and Borneo are most likely the area of origin for the most recent common ancestor of the Dissochaeteae and for many of the early diverging clades of some genera within Southeast Asia.

Fossilization processes have little impact on tip‐calibrated divergence time analyses

AbstractThe importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total‐evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non‐random distribution of missing data. The impact of non‐random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip‐calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimize the impact of taphonomy on divergence time estimation.

Integrative phylogenomics reveals a Permian origin of Adephaga beetles

AbstractBeetles are arguably the most diverse group of animals on Earth with over 400 000 described species. Yet the timing of main diversification events among these insects remains debated. The use of phylogenomic data generated using next‐generation sequencing recently resolved most recalcitrant phylogenetic relationships across Coleoptera. However, limited taxon sampling for some major clades still prevents the use of important fossil calibrations that could provide more accurate estimates of the timing of lineage diversification events among beetles. Here, we present a new fossil‐based dated framework with a focus on the suborder Adephaga. We rely on an integrative phylogenomic approach using a combination of genomic, ultraconserved element and RNAseq transcriptomic datasets, further revealing the prevalent exonic nature of ultraconserved elements in Coleoptera. We infer a robust phylogenomic tree under various optimality criteria and analytical conditions. Our preferred phylogenetic reconstruction is consistent with those of previous phylogenomic studies in recovering the paraphyly of ‘Hydradephaga’, Gyrinidae as sister to all other Adephaga, the monophyly of Geadephaga and Haliplidae as sister to a monophyletic Dytiscoidea. We further recover strong support for paraphyly of Aspidytidae and the placement of Hygrobiidae as part of a clade comprising Aspidytes, Ribera, Beutel, Balke & Vogler, Sinaspidytes Balke, Beutel & Ribera and Amphizoidae. Using 23 carefully chosen fossil calibrations across Coleoptera, we infer the origin of modern beetles ca. 317 Ma in the mid‐Carboniferous, the divergence between Archostemata and Adephaga ca. 296 Ma in the early Permian, and the crown of Adephaga in the end‐Permian ca. 255 Ma. Importantly, our analyses provide more precise estimates of divergence times for internal splits within Adephaga, including ground beetles, tiger beetles and aquatic adephagan lineages. These results represent a major step forward in our understanding of beetle diversification and will serve as a fundamental framework to unravel the evolutionary history of many clades within Adephaga.

Combining molecular datasets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)

AbstractExtant members of the ancient insect order of stoneflies exhibit a disjunct, antitropical distribution, with one major lineage exclusively occurring in the Southern Hemisphere and the other, with few exceptions, on the Northern continents. Here, we address the biogeographic distribution and phylogenetic relationships of stoneflies using a phylogenetic workflow that combines both transcriptomic and Sanger sequence datasets with heterogeneous taxon coverage. We used a dataset comprising 2997 genes derived from the transcriptomes of 30 species and Sanger sequences of seven genes for 498 species. The backbone phylogeny was mainly inferred from the transcriptomic data, whereas the Sanger nucleotide sequence data provided high species density for divergence time estimation and diversification analyses. Our results show that the biogeographic pattern we observe today is primarily more likely shaped by long‐distance over‐land dispersal than by vicariance. We inferred that the ancestors of extant stoneflies originated in the Northern Hemisphere approximately 265 Ma and were presumably restricted to this area due to climatic and geographic boundaries. Our analyses suggest that with the break‐up of Pangaea around 200 Ma and the associated climatic and geographical changes, two groups of stoneflies, the Anarctoperlaria and the Notonemouridae, dispersed to Gondwana and subsequently went extinct on the northern continents. Both groups likely dispersed across Gondwana before its break‐up into the modern continents. At least one member of another group of ‘northern’ stoneflies, the Acroneuriinae, seems to have migrated from North America to South America around 67 Ma. We found four major net diversification rate shifts, indicating rapid radiation patterns that hampered a robust phylogenetic placement of these stonefly groups. Our study provides the first conclusive evolutionary explanation for the unique distribution pattern of stoneflies.