Cretaceous environmental changes led to high extinction rates in a hyperdiverse beetle family

Evolution across the adaptive landscape in a hyperdiverse beetle radiation

The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.

Comparative mitogenome research revealed the phylogenetics and evolution of the superfamily Tenebrionoidea (Coleoptera: Polyphage)

Despite the worldwide distribution and rich diversity of the superfamily Tenebrionoidea, the knowledge of the mitochondrial genomes (mtgenome) characteristics of the superfamily is still very limited, and its phylogenetics and evolution remain unresolved. In the present study, we newly sequenced mtgenomes from 19 species belonging to Tenebrionoidea, and a total of 90 mitochondrial genomes from 16 families of Tenebrionoidea were used for phylogenetic analysis. There exist 37 genes for all 82 species of complete mtgenomes of 16 families investigated, and their characteristics are identical as reported mtgenomes of other Tenebrionoids. The Ka/Ks analysis suggests that all 13 PCGs have undergone a strong purifying selection. The phylogenetic analysis suggests the monophyly of Mordellidae, Meloidae, Oedemeridae, Pyrochroidae, Salpingidae, Scraptiidae, Lagriidae, and Tenebrionidae, and the Mordellidae is close to the Ripiphoridae. The "Tenebrionidae clade" and "Meloidae clade" are monophyletic, and both of them are sister groups. In the "Meloidae clade," Meloidae is close to Anthicidae. In the "Tenebrionidae clade," the family Lagriidae and Tenebrionidae are sister groups. The divergence time analysis suggests that Tenebrionoidea originated in the late Jurassic, Meloidae Mordellidae, Lagriidae, and Tenebrionidae in the Cretaceous, Oedemeridae in Paleogene. The work lays a base for the study of mtgenome, phylogenetics, and evolution of the superfamily Tenebrionoidea.

Phylogenomics of darkling beetles (Coleoptera: Tenebrionidae) from the Atacama Desert

Background

Tenebrionidae (Insecta: Coleoptera) are a conspicuous component of desert fauna worldwide. In these ecosystems, they are significantly responsible for nutrient cycling and show remarkable morphological and physiological adaptations. Nevertheless, Tenebrionidae colonizing individual deserts have repeatedly emerged from different lineages. The goal of our study was to gain insights into the phylogenetic relationships of the tenebrionid genera from the Atacama Desert and how these taxa are related to the globally distributed Tenebrionidae.

Methods

We used newly generated transcriptome data (47 tribes, 7 of 11 subfamilies) that allowed for a comprehensive phylogenomic analysis of the tenebrionid fauna of this hyperarid desert and fills a gap in our knowledge of the highly diversified Tenebrionidae. We examined two independent data sets known to be suitable for phylogenomic reconstructions. One is based on 35 neuropeptide precursors, the other on 1,742 orthologous genes shared among Coleoptera.

Results

The majority of Atacama genera are placed into three groups, two of which belong to typical South American lineages within the Pimeliinae. While the data support the monophyly of the Physogasterini, Nycteliini and Scotobiini, this does not hold for the Atacama genera of Edrotini, Epitragini, Evaniosomini, Praociini, Stenosini, Thinobatini, and Trilobocarini. A suggested very close relationship of Psammetichus with the Mediterranean Leptoderis also could not be confirmed. We also provide hints regarding the phylogenetic relationships of the Caenocrypticini, which occur both in South America and southern Africa. Apart from the focus on the Tenebrionidae from the Atacama Desert, we found a striking synapomorphy grouping Alleculinae, Blaptinae, Diaperinae, Stenochinae, and several taxa of Tenebrioninae, but not Tenebrio and Tribolium. This character, an insertion in the myosuppressin gene, defines a higher-level monophyletic group within the Tenebrionidae.

Conclusion

Transcriptome data allow a comprehensive phylogenomic analysis of the tenebrionid fauna of the Atacama Desert, which represents one of the seven major endemic tribal areas in the world for Tenebrionidae. Most Atacama genera could be placed in three lineages typical of South America; monophyly is not supported for several tribes based on molecular data, suggesting that a detailed systematic revision of several groups is necessary.

Fossoriality in desert-adapted tenebrionid (Coleoptera) larvae

In many extreme arid ecosystems, insects constitute major faunal components and are key contributors in nutrient cycling. Previous research on xerophily in insects has focused on adult forms. This study investigates skeletomuscular and behavioural adaptations of the Kalahari sandworm beetle larvae (Gonopus tibialis Fabricius) for dwelling in the sand. Microcomputed tomography enabled cuticle thickness distribution analysis, revealing structural reinforcements of the mandibular edge, the middle part of the head, and the ventral side of the front legs. Laboratory observations and the analysis of muscular system allowed for the definition and functional description of the elements of the digging apparatus of the sandworm larvae. Obtained results point to the crucial role of the head and mandibles in the digging process. These observations are important for understanding desert ecology and pose a challenge to develop newer excavation techniques.

The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

Species diversity of Tenebrionidae (Coleoptera) in mountaintops of extra-Andean volcanoes of Payunia (Argentina), with descriptions of two new species

The north of Neuquén province shares with the south of Mendoza province the subprovince Payunia of the biogeographical province of Patagonic steppe, which is characterized by the presence of approximately 800 volcanoes. Although we have conducted several samplings in volcanoes of Mendoza in past years to recognize the biodiversity of tenebrionids, it is still pending which is the role that these mountains have in the biota of tenebrionids in Neuquén. In this work we reported the results of two consecutive years of prospection in two volcanoes separated by 120 km between each other, Tromen and Auca Mahuida which have 3978 and 2215 meters above sea level respectively. We found that Auca Mahuida harbours a total diversity of 10 tenebrionid species and Tromen 9, but these communities were significantly different between them. From these prospections two new endemic species of Tenebrionidae are described: Scotobius aucamahuidensis Silvestro sp. nov. (Tenebrioninae: Scotobiini) from Auca Mahuida and Psectrascelis tromensis Flores sp. nov. (Pimeliinae: Nycteliini) from Tromen. Photographs for these two new species are included, with comparisons to other known species of these genera. Based on these results we discuss the role of different factors that influence tenebrionid diversity and their implications to conserve biodiversity.

Review of genus-group names in the family Tenebrionidae (Insecta, Coleoptera)

A review of genus-group names for darkling beetles in the family Tenebrionidae (Insecta: Coleoptera) is presented. A catalogue of 4122 nomenclaturally available genus-group names, representing 2307 valid genera (33 of which are extinct) and 761 valid subgenera, is given. For each name the author, date, page number, gender, type species, type fixation, current status, and first synonymy (when the name is a synonym) are provided. Genus-group names in this family are also recorded in a classification framework, along with data on the distribution of valid genera and subgenera within major biogeographical realms. A list of 535 unavailable genus-group names (e.g., incorrect subsequent spellings) is included. Notes on the date of publication of references cited herein are given, when known.

The following genera and subgenera are made available for the first time: Anemiadena Bouchard & Bousquet, subgen. nov. (in Cheirodes Gené, 1839), Armigena Bouchard & Bousquet, subgen. nov. (in Nesogena Mäklin, 1863), Debeauxiella Bouchard & Bousquet, subgen. nov. (in Hyperops Eschscholtz, 1831), Hyperopsis Bouchard & Bousquet, subgen. nov. (in Hyperops Eschscholtz, 1831), Linio Bouchard & Bousquet, subgen. nov. (in Nilio Latreille, 1802), Matthewsotys Bouchard & Bousquet, gen. nov., Neosolenopistoma Bouchard & Bousquet, subgen. nov. (in Eurynotus W. Kirby, 1819), Paragena Bouchard & Bousquet, subgen. nov. (in Nesogena Mäklin, 1863), Paulianaria Bouchard & Bousquet, gen. nov., Phyllechus Bouchard & Bousquet, gen. nov., Prorhytinota Bouchard & Bousquet, subgen. nov. (in Rhytinota Eschscholtz, 1831), Pseudorozonia Bouchard & Bousquet, subgen. nov. (in Rozonia Fairmaire, 1888), Pseudothinobatis Bouchard & Bousquet, gen. nov., Rhytinopsis Bouchard & Bousquet, subgen. nov. (in Thalpophilodes Strand, 1942), Rhytistena Bouchard & Bousquet, subgen. nov. (in Rhytinota Eschscholtz, 1831), Spinosdara Bouchard & Bousquet, subgen. nov. (in Osdara Walker, 1858), Spongesmia Bouchard & Bousquet, subgen. nov. (in Adesmia Fischer, 1822), and Zambesmia Bouchard & Bousquet, subgen. nov. (in Adesmia Fischer, 1822).

The names Adeps Gistel, 1857 and Adepsion Strand, 1917 syn. nov. [= Tetraphyllus Laporte & Brullé, 1831], Asyrmatus Canzoneri, 1959 syn. nov. [= Pystelops Gozis, 1910], Euzadenos Koch, 1956 syn. nov. [= Selenepistoma Dejean, 1834], Gondwanodilamus Kaszab, 1969 syn. nov. [= Conibius J.L. LeConte, 1851], Gyrinodes Fauvel, 1897 syn. nov. [= Nesotes Allard, 1876], Helopondrus Reitter, 1922 syn. nov. [= Horistelops Gozis, 1910], Hybonotus Dejean, 1834 syn. nov. [= Damatris Laporte, 1840], Iphthimera Reitter, 1916 syn. nov. [= Metriopus Solier, 1835], Lagriomima Pic, 1950 syn. nov. [= Neogria Borchmann, 1911], Orphelops Gozis, 1910 syn. nov. [= Nalassus Mulsant, 1854], Phymatium Billberg, 1820 syn. nov. [= Cryptochile Latreille, 1828], Prosoblapsia Skopin & Kaszab, 1978 syn. nov. [= Genoblaps Bauer, 1921], and Pseudopimelia Gebler, 1859 syn. nov. [= Lasiostola Dejean, 1834] are established as new synonyms (valid names in square brackets). Anachayus Bouchard & Bousquet, nom. nov. is proposed as a replacement name for Chatanayus Ardoin, 1957, Genateropa Bouchard & Bousquet, nom. nov. as a replacement name for Apterogena Ardoin, 1962, Hemipristula Bouchard & Bousquet, nom. nov. as a replacement name for Hemipristis Kolbe, 1903, Kochotella Bouchard & Bousquet, nom. nov. as a replacement name for Millotella Koch, 1962, Medvedevoblaps Bouchard & Bousquet, nom. nov. as a replacement name for Protoblaps G.S. Medvedev, 1998, and Subpterocoma Bouchard & Bousquet, nom. nov. is proposed as a replacement name for Pseudopimelia Motschulsky, 1860. Neoeutrapela Bousquet & Bouchard, 2013 is downgraded to a subgenus (stat. nov.) of Impressosora Pic, 1952. Anchomma J.L. LeConte, 1858 is placed in Stenosini: Dichillina (previously in Pimeliinae: Anepsiini); Entypodera Gerstaecker, 1871, Impressosora Pic, 1952 and Xanthalia Fairmaire, 1894 are placed in Lagriinae: Lagriini: Statirina (previously in Lagriinae: Lagriini: Lagriina); Loxostethus Triplehorn, 1962 is placed in Diaperinae: Diaperini: Diaperina (previously in Diaperinae: Diaperini: Adelinina); Periphanodes Gebien, 1943 is placed in Stenochiinae: Cnodalonini (previously in Tenebrioninae: Helopini); Zadenos Laporte, 1840 is downgraded to a subgenus (stat. nov.) of the older name Selenepistoma Dejean, 1834.

The type species [placed in square brackets] of the following available genus-group names are designated for the first time: Allostrongylium Kolbe, 1896 [Allostrongyliumsilvestre Kolbe, 1896], Auristira Borchmann, 1916 [Auristiraoctocostata Borchmann, 1916], Blapidocampsia Pic, 1919 [Campsiapallidipes Pic, 1918], Cerostena Solier, 1836 [Cerostenadeplanata Solier, 1836], Coracostira Fairmaire, 1899 [Coracostiraarmipes Fairmaire, 1899], Dischidus Kolbe, 1886 [Helopssinuatus Fabricius, 1801], Eccoptostoma Gebien, 1913 [Taraxidesruficrus Fairmaire, 1894], Ellaemus Pascoe, 1866 [Emcephalussubmaculatus Brême, 1842], Epeurycaulus Kolbe, 1902 [Epeurycaulusaldabricus Kolbe, 1902], Euschatia Solier, 1851 [Euschatiaproxima Solier, 1851], Heliocaes Bedel, 1906 [Blaps emarginata Fabricius, 1792], Hemipristis Kolbe, 1903 [Hemipristisukamia Kolbe, 1903], Iphthimera Reitter, 1916 [Stenocararuficornis Solier, 1835], Isopedus Stein, 1877 [Helopstenebrioides Germar, 1813], Malacova Fairmaire, 1898 [Malacovabicolor Fairmaire, 1898], Modicodisema Pic, 1917 [Disemasubopaca Pic, 1912], Peltadesmia Kuntzen, 1916 [Metriopusplatynotus Gerstaecker, 1854], Phymatium Billberg, 1820 [Pimeliamaculata Fabricius, 1781], Podoces Péringuey, 1886 [Podocesgranosula Péringuey, 1886], Pseuduroplatopsis Pic, 1913 [Borchmanniajavana Pic, 1913], Pteraulus Solier, 1848 [Pteraulussulcatipennis Solier, 1848], Sciaca Solier, 1835 [Hylithusdisctinctus Solier, 1835], Sterces Champion, 1891 [Stercesviolaceipennis Champion, 1891] and Teremenes Carter, 1914 [Tenebriolongipennis Hope, 1843].

Evidence suggests that some type species were misidentified. In these instances, information on the misidentification is provided and, in the following cases, the taxonomic species actually involved is fixed as the type species [placed in square brackets] following requirements in Article 70.3 of the International Code of Zoological Nomenclature: Accanthopus Dejean, 1821 [Tenebriovelikensis Piller & Mitterpacher, 1783], Becvaramarygmus Masumoto, 1999 [Dietysusnodicornis Gravely, 1915], Heterophaga Dejean, 1834 [Opatrumlaevigatum Fabricius, 1781], Laena Dejean, 1821, [Scaurusviennensis Sturm, 1807], Margus Dejean, 1834 [Colydiumcastaneum Herbst, 1797], Pachycera Eschscholtz, 1831 [Tenebriobuprestoides Fabricius, 1781], Saragus Erichson, 1842 [Celibecostata Solier, 1848], Stene Stephens, 1829 [Colydiumcastaneum Herbst, 1797], Stenosis Herbst, 1799 [Tageniaintermedia Solier, 1838] and Tentyriopsis Gebien, 1928 [Tentyriopsispertyi Gebien, 1940].

The following First Reviser actions are proposed to fix the precedence of names or nomenclatural acts (rejected name or act in square brackets): Stenosisciliaris Gebien, 1920 as the type species for Afronosis G.S. Medvedev, 1995 [Stenosisleontjevi G.S. Medvedev, 1995], Alienoplonyx Bremer, 2019 [Alienolonyx], Amblypteraca Mas-Peinado, Buckley, Ruiz & García-París, 2018 [Amplypteraca], Caenocrypticoides Kaszab, 1969 [Caenocripticoides], Deriles Motschulsky, 1872 [Derilis], Eccoptostira Borchmann, 1936 [Ecoptostira], †Eodromus Haupt, 1950 [†Edromus], Eutelus Solier, 1843 [Lutelus], Euthriptera Reitter, 1893 [Enthriptera], Meglyphus Motschulsky, 1872 [Megliphus], Microtelopsis Koch, 1940 [Extetranosis Koch, 1940, Hypermicrotelopsis Koch, 1940], Neandrosus Pic, 1921 [Neoandrosus], Nodosogylium Pic, 1951 [Nodosogilium], Notiolesthus Motschulsky, 1872 [Notiolosthus], Pseudeucyrtus Pic, 1916 [Pseudocyrtus], Pseudotrichoplatyscelis Kaszab, 1960 [Pseudotrichoplatynoscelis and Pseudotrichoplatycelis], Rhydimorpha Koch, 1943 [Rhytimorpha], Rhophobas Motschulsky, 1872 [Rophobas], Rhyssochiton Gray, 1831 [Ryssocheton and Ryssochiton], Sphaerotidius Kaszab, 1941 [Spaerotidius], Stira Agassiz, 1846 (Mollusca) [Stira Agassiz, 1846 (Coleoptera)], Sulpiusoma Ferrer, 2006 [Sulpiosoma] and Taenobates Motschulsky, 1872 [Taeniobates].

Supporting evidence is provided for the conservation of usage of Cyphaleus Westwood, 1841 nomen protectum over Chrysobalus Boisduval, 1835 nomen oblitum.

Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs

Tribolium castaneum, the red flour beetle, is among the most well-studied eukaryotic genetic model organisms. Tribolium often serves as a comparative bridge from highly derived Drosophila traits to other organisms. Simultaneously, as a member of the most diverse order of metazoans, Coleoptera, Tribolium informs us about innovations that accompany hyper diversity. However, understanding the tempo and mode of evolutionary innovation requires well-resolved, time-calibrated phylogenies, which are not available for Tribolium. The most recent effort to understand Tribolium phylogenetics used two mitochondrial and three nuclear markers. The study concluded that the genus may be paraphyletic and reported a broad range for divergence time estimates. Here we employ recent advances in Bayesian methods to estimate the relationships and divergence times among Tribolium castaneum, T. brevicornis, T. confusum, T. freemani, and Gnatocerus cornutus using 1368 orthologs conserved across all five species and an independent substitution rate estimate. We find that the most basal split within Tribolium occurred ~86 Mya [95% HPD 85.90-87.04 Mya] and that the most recent split was between T. freemani and T. castaneum at ~14 Mya [95% HPD 13.55-14.00]. Our results are consistent with broader phylogenetic analyses of insects and suggest that Cenozoic climate changes played a role in the Tribolium diversification.

Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects

Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early-Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.

Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction.IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.

The Fossil Record of Darkling Beetles (Insecta: Coleoptera: Tenebrionidae)

The fossil record of Tenebrionidae (excluding the Quartenary) is presented. In total, 122 fossil species, clearly belonging to the family, are known; some beetles were determined only to genus; 78 genera are listed in the fossil record, including 29 extinct genera. The great diversity of tenebrionids occurs in the Lower Cretaceous Lagerstätte of China (Yixian Formation), Middle Paleocene of France (Menat), Lower Eocene deposits of Germany (Geiseltal), Upper Eocene Baltic amber (Eastern Europe), Upper Eocene deposits of Florissant Formation (USA) and Miocene (Dominican amber). Tenebrionids of the following major lineages, including seven subfamilies, are currently known in the fossil record. These include the lagrioid branch (Lagriinae, Nilioninae), pimelioid branch (Pimeliinae), and tenebrioid branch (Alleculinae, Tenebrioninae, Diaperinae, Stenochiinae). The importance of the fossil record for evolutionary reconstructions and phylogenetic patterns is discussed. The oldest Jurassic and Early Cretaceous darkling beetles of the tenebrionoid branch consist of humid-adapted groups from the extant tribes Alleculini, Ctenopodiini (Alleculinae), and Alphitobiini (Tenebrioninae). Thus, paleontological evidence suggests that differentiation of the family started at least by the Middle Jurassic but does not indicate that xerophilic darkling beetles differentiated much earlier than mesophilic groups.

Phylogenetic revision of the psammophilic Trogloderus LeConte (Coleoptera: Tenebrionidae), with biogeographic implications for the Intermountain Region

The genus Trogloderus LeConte, 1879, which is restricted to dunes and sandy habitats in the western United States, is revised using morphological and molecular information. Six new species are described from desert regions: Trogloderus arcanus New Species (Lahontan Trough); Trogloderus kandai New Species (Owens Valley); Trogloderus major New Species (Mohave Desert); Trogloderus skillmani New Species (eastern Great Basin and Mohave Desert); Trogloderus verpus New Species (eastern Colorado Plateau); and Trogloderus warneri New Species (western Colorado Plateau). A molecular phylogeny is presented for the genus and used to infer its historical biogeography. The most recent common ancestor of Trogloderus is dated to 5.2 mya and is inferred to have inhabited the Colorado Plateau. Current species most likely arose during the mid-Pleistocene where the geographic features of the Lahontan Trough, Bouse Embayment and Kaibab Plateau were significant factors driving speciation.

Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the 'time-area', 'tropical niche conservatism', 'ecological limits' and 'evolutionary speed' hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns.

Fossil evidence reveals how plants responded to cooling during the Cretaceous-Paleogene transition

BACKGROUND

Around the Cretaceous-Paleogene (K-Pg) boundary, an obvious global cooling occurred, which resulted in dramatic changes in terrestrial ecosystems and the evolutionary trends of numerous organisms. However, how plant lineages responded to the cooling has remained unknown until now. Between ca. 70-60 Ma Mesocyparis McIver & Basinger (Cupressaceae), an extinct conifer genus, was distributed from eastern Asia to western North America and provides an excellent opportunity to solve this riddle.

RESULTS

Here we report a new species, Mesocyparis sinica from the early Paleocene of Jiayin, Heilongjiang, northeastern China. By integrating lines of evidence from phylogeny and comparative morphology of Mesocyparis, we found that during ca.70-60 Ma, the size of seed cone of Mesocyparis more than doubled, probably driven by the cooling during the K-Pg transition, which might be an effective adaptation for seed dispersal by animals. More importantly, we discovered that the northern limit of this genus, as well as those of two other arboreal taxa Metasequoia Miki ex Hu et Cheng (gymnosperm) and Nordenskioldia Heer (angiosperm), migrated ca.4-5° southward in paleolatitude during this time interval.

CONCLUSIONS

Our results suggest that the cooling during the K-Pg transition may have been responsible for the increase in size of the seed cone of Mesocyparis and have driven the migration of plants southwards.

Diversification shifts in leafroller moths linked to continental colonization and the rise of angiosperms

Tectonic dynamics and niche availability play intertwined roles in determining patterns of diversification. Such drivers explain the current distribution of many clades, whereas events such as the rise of angiosperms can have more specific impacts, such as on the diversification rates of herbivores. The Tortricidae, a diverse group of phytophagous moths, are ideal for testing the effects of these determinants on the diversification of herbivorous clades. To estimate ancestral areas and diversification patterns in Tortricidae, a complete tribal-level dated tree was inferred using molecular markers (one mitochondrial and five nuclear) and calibrated using fossil constraints. We found that Tortricidae diverged from their sister group c. 120 Myr ago (Ma) and diversified c. 97 Ma, a timeframe synchronous with the rise of angiosperms in the Early-mid Cretaceous. Ancestral areas analysis, based on updated Wallace's biogeographical regions, supports the hypothesis of a Gondwanan origin of Tortricidae in the South American plate. We also detected an increase in speciation rate that coincided with the peak of angiosperm diversification in the Cretaceous. This in turn probably was further heightened by continental colonization of the Palaeotropics when angiosperms became dominant by the end of the Late Cretaceous.

Karyotype and sex chromosome differentiation in two Nalassus species (Coleoptera, Tenebrionidae)

Cytogenetic features of Nalassus bozdagus Nabozhenko & Keskin, 2010 and Nalassus plebejus Küster, 1850 were analysed using conventional and differential staining. Mitotic and meiotic chromosomal analysis revealed the diploid number as 2n = 20 (9+Xy_p) in both species. Besides the general resemblance of two Nalassus Mulsant, 1854 karyotypes, important differences related to variations in the number of metacentric/submetacentric chromosomes, localization of highly impregnated regions which are considered as NOR and heterochromatin distribution are clearly observed. The most prominent difference between two species is found related to the X chromosome which is clearly larger in Nalassus bozdagus and has a conspicuous secondary constriction on the long arm. As a result of silver staining, the existence of highly impregnated areas associated with Xy_p of Nalassus bozdagus in both prophase I and metaphase I, suggests that NORs are seemingly located on sex chromosomes. On the other hand, the potential NORs of Nalassus plebejus were observed only in prophase I nuclei. With the application of fluorescence dye DAPI, the AT rich chromosome regions and Xy_p which forms the parachute configuration were shown in both species.

Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

PREMISE OF THE STUDY

The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation.

METHODS

Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny.

KEY RESULTS

Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma).

CONCLUSIONS

These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.

Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

Evolution of Spermophagus seed beetles (Coleoptera, Bruchinae, Amblycerini) indicates both synchronous and delayed colonizations of host plants

Seed beetles are a group of specialized chrysomelid beetles, which are mostly associated with plants of the legume family (Fabaceae). In the legume-feeding species, a marked trend of phylogenetic conservatism of host use has been highlighted by several molecular phylogenetics studies. Yet, little is known about the evolutionary patterns of association of species feeding outside the legume family. Here, we investigate the evolution of host use in Spermophagus, a species-rich seed beetle genus that is specialized on two non-legume host-plant groups: morning glories (Convolvulaceae) and mallows (Malvaceae: Malvoideae). Spermophagus species are widespread in the Old World, especially in the Afrotropical, Indomalaya and Palearctic regions. In this study we rely on eight gene regions to provide the first phylogenetic framework for the genus, along with reconstructions of host use evolution, estimates of divergence times and historical biogeography analyses. Like the legume-feeding species, a marked trend toward conservatism of host use is revealed, with one clade specializing on Convolvulaceae and the other on Malvoideae. Comparisons of plants' and insects' estimates of divergence times yield a contrasted pattern: on one hand a quite congruent temporal framework was recovered for morning-glories and their seed-predators; on the other hand the diversification of Spermophagus species associated with mallows apparently lagged far behind the diversification of their hosts. We hypothesize that this delayed colonization of Malvoideae can be accounted for by the respective biogeographic histories of the two groups.

Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Background

Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads.

Results

Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior.

Conclusions

These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.