Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation

Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen

The timing, sequence, and scale of uplift of the Himalayan-Tibetan Orogen (HTO) are controversially debated. Many geoscientific studies assume paleoelevations close to present-day elevations and the existence of alpine environments across the HTO already in the late Paleogene, contradicting fossil data. Using molecular genetic data of ground beetles, we aim to reconstruct the paleoenvironmental history of the HTO, focusing on its southern margin (Himalayas, South Tibet). Based on a comprehensive sampling of extratropical Carabus, and ~ 10,000 bp of mitochondrial and nuclear DNA we applied Bayesian and Maximum likelihood methods to infer the phylogenetic relationships. We show that Carabus arrived in the HTO at the Oligocene-Miocene boundary. During the early Miocene, five lineages diversified in different parts of the HTO, initially in its southern center and on its eastern margin. Evolution of alpine taxa occurred during the late Miocene. There were apparently no habitats for Carabus before the late Oligocene. Until the Late Oligocene elevations must have been low throughout the HTO. Temperate forests emerged in South Tibet in the late Oligocene at the earliest. Alpine environments developed in the HTO from the late Miocene and, in large scale, during the Pliocene-Quaternary. Findings are consistent with fossil records but contrast with uplift models recovered from stable isotope paleoaltimetry.

Molecular and biometric data on Carabus (Macrothorax) morbillosus Fabricius, 1792 (Coleoptera, Carabidae) from Mid Mediterranean areas

The present study was carried out using molecular and biometric data of Carabus (Macrothorax) morbillosus from mid-Mediterranean areas to determine additional information on basal relationships among its representative subspecies. To this aim, two different kinds of approach were employed, including a morphometric analysis of four morphological parameters (i.e., elytra length, elytra width, pronotum length, pronotum width) of 128 specimens, and a Bayesian genetic analysis of 44 cytochrome oxidase subunit I (COI) partial sequences (i.e., 38 examined for the first time and six retrieved from GenBank database). Representative populations of C. (M.) morbillosus were sampled in four countries, namely Italy, Malta, Spain, and Tunisia. The present findings support the validity of four C. (M.) morbillosus subspecies, specifically C. (M.) m. alternans, C. (M.) m. bruttianus, C. (M.) m. constantinus, and C. (M.) m. macilentus, and redefine these subspecies' distributions. Notably, within the C. (M.) m. constantinus clade, two (i.e., Sardinia/Tuscany and Lampedusa) out of the three subgroups appear as homogeneous geographical groupings.

From monocots to dicots: host shifts in Afrotropical derelomine weevils shed light on the evolution of non-obligatory brood pollination mutualism

Weevils from the tribe Derelomini (Curculionidae: Curculioninae) are specialized brood pollinators engaged in mutualistic relationships with several angiosperm lineages. In brood pollination systems, reproductive plant tissues are used for the development of insect larval stages, whereas adult insects pollinate their plant hosts as a reward. The evolutionary history of derelomines in relationship to their hosts is poorly understood and potentially contrasts with other brood pollination systems, wherein a pollinator lineage is usually associated with a single host plant family. In the case of Afrotropical Derelomini, host records indicate a diverse host repertoire consisting of several families of monocot and dicot plants. In this study, we investigate their phylogenetic relationships, timing of diversification and evolution of host use. Our results suggest that derelomine lineages started their diversification ~40 Mya. Reconstructions of host use evolution support an ancestral association with the monocotyledonous palm family (Arecaceae), followed by several shifts towards other plant families in Afrotropical lineages, especially to dicotyledonous plants from the family Ebenaceae (on the genus Euclea L.). Some level of phylogenetic conservatism of host use is recovered for the lineages associated with either palms or Euclea. Multiple instances of sympatric weevil assemblages on the same plant are also unravelled, corresponding to either single or independent colonization events. Overall, the diversity of hosts colonized and the frequency of sympatric assemblages highlighted in non-obligatory plant–derelomine brood pollination systems contrast with what is generally expected from plant–insect brood pollination systems.

Dispersal ability and its consequences for population genetic differentiation and diversification

Dispersal ability is known to influence geographical structuring of genetic variation within species, with a direct relationship between low vagility and population genetic structure, which can potentially give rise to allopatric speciation. However, our general understanding of the relationship between dispersal ability, population differentiation and lineage diversification is limited. To address this issue, we sampled mitochondrial DNA variation within lineages of beetles and spiders across the Canary Islands to explore the relationships between dispersal ability, differentiation within lineages and diversification. We found positive relationships between population genetic structure and diversification for both beetles and spiders. Comparisons between dispersive and non-dispersive lineages revealed significant differences for both lineage differentiation and diversification. For both taxa, non-dispersive lineages had stronger population genetic structure. Genus-level endemic species richness and proxies for diversification rate within genera were higher in non-dispersive taxa for both beetles and spiders. Comparisons of average and maximum node divergences within genera suggest that species turnover may be higher in non-dispersive genera. Our results reveal a model where dispersal limitation may shape the diversity of lineages across evolutionary timescales by positively influencing intraspecific and species diversity, moderated by higher extinction rates compared to more dispersive lineages.

Complex co-evolutionary relationships between cicadas and their symbionts

Previous evidence suggests that cicadas lacking Hodgkinia may harbour the yeast-like fungal symbionts (YLS). Here, we reinforce an earlier conclusion that the pathogenic ancestor of YLS independently infected different cicada lineages instead of the common ancestor of Cicadidae. Five independent replacement events in the loss of Hodgkinia/acquisition of YLS and seven other replacement events of YLS (from an Ophiocordyceps fungus to another Ophiocordyceps fungus) are hypothesised to have occurred within the sampled cicada taxa. The divergence time of YLS lineages was later than that of corresponding cicada lineages. The rapid shift of diversification rates of YLS and related cicada-parasitizing Ophiocordyceps began at approximately 32.94 Ma, and the diversification rate reached the highest value at approximately 24.82 Ma, which corresponds to the cooling climate changes at the Eocene-Oligocene boundary and the Oligocene-Miocene transition respectively. Combined with related acquisition/replacement events of YLS occurred during the cooling-climate periods, we hypothesise that the cooling-climate changes impacted the interactions between cicadas and related Ophiocordyceps, which coupled with the unusual life cycle and the differentiation of cicadas may finally led to the diversification of YLS in Cicadidae. Our results contribute to a better understanding of the evolutionary transition of YLS from entomopathogenic fungi in insects.

Global dispersal and diversification in ground beetles of the subfamily Carabinae

The origin and diversification process of lineages of organisms that are currently widely distributed among continents is an interesting subject for exploring the evolutionary history of global species diversity. Ground beetles of the subfamily Carabinae are flightless except for one lineage, but nevertheless occur on all continents except Antarctica. Here, we used sequence data from ultraconserved elements to reconstruct the phylogeny, divergence time, biogeographical history, ancestral state of hind wings and changes in the speciation rate of Carabinae. Our results show that Carabinae originated in the Americas and diversified into four tribes during the period from the late Jurassic to the late Cretaceous, with two in South America (Celoglossini) and Australasia (Pamborini) and two in Laurasia (Cychrini and Carabini). The ancestral Carabinae were inferred to be winged; three of four tribes (Cychrini, Ceglossini and Pamborini) have completely lost their hind wings and flight capability. The remaining tribe, Carabini, diverged into the subtribes Carabina (wingless) and Calosomina (winged) in the Oligocene. Carabina originated in Europe, spread over Eurasia and diversified into approximately 1000 species, accounting for around 60% of all Carabinae species. Calosomina that were flight-capable dispersed from North America or Eurasia to South America, Australia, and Africa, and then flightless lineages evolved on oceanic islands and continental highlands. The speciation rate increased in the Cychrini and Carabini clades in Eurasia. Within Carabini, the speciation rate was higher for wingless than winged states. Our study showed that the global distribution of Carabinae resulted from ancient dispersal before the breakup of Gondwana and more recent dispersal through flight around the world. These patterns consequently illustrate the causal relationships of geographical history, evolution of flightlessness, and the global distribution and species diversity of Carabinae.

Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis

Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.

Underestimated diversity: Cryptic species and phylogenetic relationships in the subgenus Cobalius (Coleoptera: Hydraenidae) from marine rockpools

Marine rockpools are isolated patches of habitat in the supratidal environment (the so-called splash zone), at the transition between sea and land, found along the rocky shores worldwide and characterized by harsh conditions for life. Nonetheless, few specialized invertebrates successfully colonized this peculiar environment. Among them several members of the water beetles Ochthebius Leach, 1815, subgenus Cobalius Rey (1886), which are found almost exclusively in supratidal and upper-most intertidal marine rockpools from the eastern Atlantic Ocean (Cape Verde, Canary Islands and Morocco, Madeira, Azores) throughout the whole Mediterranean basin. The subgenus Cobalius before 2020 was considered to include ten valid species, based on morphological differences. In late 2020, four additional new species were described. However, recent molecular phylogenetic studies have uncovered further cryptic diversity suggesting the presence of multiple undetected species within this group, highlighting that the species boundaries remain unclear and systematics and taxonomy are in need of revision. In this study we provide a molecular phylogeny based on DNA sequence data from mitochondrial and nuclear genes obtained from ten described species belonging to the subgenus Cobalius, and extensive taxon sampling, in order to better understand the phylogenetic relationships within this genus and to infer the biogeographic processes behind its diversification. We also used a molecular clock to define a time window for diversification of distinct clades within the subgenus, and explore aspects of its evolutionary history. Finally, we used three species delimitation methods (PTP, GMYC and ABGD) to clarify taxonomy and validate species boundaries. Our phylogenetic and biogeographic results identified sixteen independent lineages grouped in four main clades and the possible origin of Cobalius was estimated to be in the Early Miocene (~22 Mya) in W Mediterranean area. Moreover, species delimitation methods suggest there are between 16 and 24 putative species, most of them diverged during the Late Miocene, Pliocene and Pleistocene (6.0-0.11 Mya).

Ancient relicts or recent immigrants? Different dating strategies alter diversification scenarios of New Zealand aquatic beetles (Coleoptera: Hydrophilidae: Berosus)

Dated species-level phylogenies are crucial for understanding the origin and evolutionary history of modern faunas, yet difficult to obtain due to the frequent absence of suitable age calibrations at species level. Substitution rates of related or more inclusive clades are often used to overcome this limitation but the accuracy of this approach remains untested. We compared tree dating based on substitution rates with analyses implementing fossil data by direct node-dating and indirect root-age constraints for the New Zealand endemic Berosus water beetles (Coleoptera: Hydrophilidae). The analysis based solely on substitution rates indicated a Miocene colonization of New Zealand and Pleistocene origin of species. By contrast, all analyses that implemented fossil data resulted in significantly older age estimates, indicating an ancient early Cenozoic origin of the New Zealand clade, diversification of species during or after the Oligocene transgression and Miocene-Pliocene origin of within-species population structure. Rate-calibrated time trees were incongruent with recently published Coleoptera time trees, the fossil record of Berosus and the distribution of outgroup species. Strong variation of substitution rates among Coleoptera lineages, as well as among lineages within the family Hydrophilidae, was identified as the principal reason for low accuracy of rate-calibrated analyses, resulting in underestimated node ages in Berosus. We provide evidence that Oligocene to Pliocene events, rather than the Pleistocene Glacial cycles, played an essential role in the formation of the modern New Zealand insect fauna.

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma  burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

Chronological Incongruences between Mitochondrial and Nuclear Phylogenies of Aedes Mosquitoes

One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoes.

High molecular diversity in Carabus (Hygrocarabus) variolosus and C. nodulosus

The Carabus subgenus Hygrocarabus contains two taxa: C. variolosus and C. nodulosus, the species or subspecies status of which is handled far from uniform in the literature. Both taxa show a similar morphology, the shape of the tip of the aedeagus provides a reliable morphological marker for identification. We analysed two mitochondrial gene parts (COI-5’ and COI-3’) and a nuclear one (ITS2). High diversity was found showing specific geographical patterns. Introgressive hybridisation was detected but interpreted not as an argument for subspecies status because high genetic distances indicated that it must have taken place in former times. In a laboratory hybridisation experiment, the male did not accept the female of the other taxon, supporting the conclusion that these are separate species. A series of refuges was expected for the period of ice ages. Although only the taxon C. variolosus is listed in Annex II and IV of the EU Habitats Directive, C. nodulosus also falls under this listing, as at the time of including the species into the Annexes in 2004, the two taxa were considered subspecies and hence the listing would include both, independent of later taxonomic revisions.

Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California

The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e., on nunataks), while shallow divergence and limited genetic variation are assumed to result from expansion from large refugia at the edge of ice shields (i.e., massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their spatial and demographic response to glaciation, and such a simple dichotomy may obscure the localization of actual refugia. In this study, we use the Nebria ingens complex (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test how drainage basins are linked to their observed population structure. By analysing mitochondrial COI gene sequences and genome-wide single nucleotide polymorphisms, we find that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingens complex. In addition, we find that an intermediate morphotype within the N. ingens complex is the product of historical hybridization of N. riversi and N. ingens in the San Joaquin basin during glaciation. This study highlights the importance of considering ecological preferences in how species respond to climate fluctuations and provides an explanation for discordances that are often observed in comparative phylogeographical studies.

Phylogeographical analysis of character displacement in feeding phenotypes of snail-feeding Acoptolabrus ground beetles

Ecological character displacement predicts that interspecific resource competition results in greater trait divergence between species in sympatry than in allopatry. However, other processes, such as ecological sorting, result in the same pattern of trait variation. In this study, we characterize character displacement in eight species of snail-feeding Acoptolabrus ground beetles in the Far East. Acoptolabrus exhibit divergent feeding phenotypes, including species with a slender forebody that is able to intrude into large shells and species with stout heads and mandibles for crushing small shells. The pattern of character displacement in feeding phenotypes was confirmed by multivariate analysis of body dimensions. Molecular phylogenetic analysis, divergence time estimation and biogeographical analysis revealed that sympatry and phenotypic divergence occurred repeatedly during the Pleistocene and almost simultaneously within each geographical area. Comparative analysis revealed that the evolution of feeding phenotypes best fitted a selective model with three adaptive optima, corresponding to the three cases of sympatry with a congener. Repeated coincidences of sympatry and adaptive differentiation in feeding phenotypes suggested causal relationships, although the precise order of events was difficult to discriminate. This study provides insight into the spatiotemporal dynamics of interspecific interactions and adaptive phenotypic diversification.

Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari

High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.

The origin of the giant ground beetle Aplothorax burchelli on St Helena Island

Some highly isolated oceanic islands harbour endemic ground beetles that have lost the ability to fly. Here, we investigated the origin of the possibly extinct flightless giant ground beetle Aplothorax burchelli on St Helena Island in the South Atlantic. Aplothorax burchelli was initially considered to be a member of the subtribe Calosomina (=genus Calosoma) of the subfamily Carabinae (Coleoptera: Carabidae) closely related to the genus Ctenosta (=Calosoma subgenus Ctenosta), but this proposition was questioned due to its unique external and genital morphology. We conducted a phylogenetic analysis of mitogenome sequences using historical specimens of A. burchelli and samples of representative species of Carabinae. Our analysis of 13 protein-coding gene sequences revealed that A. burchelli is definitely a member of Calosomina, most closely related to a species of Ctenosta. Further analysis using NADH dehydrogenase subunit 5 gene sequences from most groups in Calosomina showed that A. burchelli formed a monophyletic group with Ctenosta species from Africa and Madagascar. Our results suggest that the ancestor of A. burchelli, which had the ability to fly, colonized St Helena from Africa after the emergence of the island 14 Mya, and has since undergone evolutionary changes in conjunction with loss of flight.

Middle Stone Age foragers resided in high elevations of the glaciated Bale Mountains, Ethiopia

Studies of early human settlement in alpine environments provide insights into human physiological, genetic, and cultural adaptation potentials. Although Late and even Middle Pleistocene human presence has been recently documented on the Tibetan Plateau, little is known regarding the nature and context of early persistent human settlement in high elevations. Here, we report the earliest evidence of a prehistoric high-altitude residential site. Located in Africa's largest alpine ecosystem, the repeated occupation of Fincha Habera rock shelter is dated to 47 to 31 thousand years ago. The available resources in cold and glaciated environments included the exploitation of an endemic rodent as a key food source, and this played a pivotal role in facilitating the occupation of this site by Late Pleistocene hunter-gatherers.

Rapid speciation and ecological divergence into North American alpine habitats: the Nippononebria (Coleoptera: Carabidae) species complex

The climate-driven species pump hypothesis has been supported in a number of phylogeographic studies of alpine species. Climate-driven shifts in distribution, coupled with rapid demographic change, have led to strong genetic drift and lineage diversification. Although the species pump has been linked to rapid speciation in a number of studies, few studies have demonstrated that ecological divergence accompanies rapid speciation. Here we examine genetic, morphological and physiological variation in members of the ground beetle taxon Nippononebria, to test three competing hypotheses of evolutionary diversification: isolation and incomplete lineage sorting (no speciation), recent speciation without ecological divergence, or recent speciation with ecological divergence into alpine habitats. Genetic data are consistent with recent divergence, with major lineages forming in the last million years. A species tree analysis, in conjunction with morphological divergence in male reproductive traits, support the formation of three recognized Nippononebria taxa. Furthermore, both morphological and physiological traits demonstrate ecological divergence in alpine lineages, with convergent shifts in body shape and thermal tolerance breadth. This provides strong evidence that the climate-driven species pump can generate ecological novelty, though it is argued that spatial scale may be a key determinant of broader patterns of macroevolution in alpine communities.

The mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer (Coleoptera, Carabidae)

The complete mitochondrial genome of the Jeju ground beetle Carabus smaragdinus monilifer was analyzed to determine its structure, morphology, and other characteristics. The 16,737-bp long mitochondrial genome consisted of 37 genes, including 13 protein-coding genes, two rRNAs, and 22 tRNAs. The order, encoding direction, and the initiation and termination codons of the 37 genes of C. smaragdinus monilifer were identical to those of other species in the family Carabidae. Phylogenetic analysis revealed that C. smaragdinus monilifer is clustered with Carabus lafossei. Herein, we have provided the complete mitochondrial genome sequence of C. smaragdinus monilifer to understand the phylogeny of Carabidae.

Orogeny, sympatry and emergence of a new genus of Alpine subterranean Trechini (Coleoptera: Carabidae)

Despite two centuries of research in European subterranean habitats, which resulted in descriptions of numerous obligate subterranean beetle species, the role of ecological differentiation in speciation of subterranean beetles remains understudied. Discovery of a new genus and a species of Alpine subterranean Trechini beetles, Petraphaenops unguiculatus gen. & sp. nov., enables us to question the reasons for its morphological and ecological divergence. Multilocus, time-calibrated phylogeny and extensive morphological analyses were used to place the evolution of the species in a temporal and palaeogeographical framework. Set within the phylogeny of Alpine Trechini, the new genus is shown to have split from its sister-genus, Aphaenopidius, by the end of the Pliocene. The timeline of the split between these closely related genera corresponds to the onset of major orogenetic events in the southern Calcareous Alps. The orogeny dynamics, coupled with simultaneous diversification of subterranean habitats, presumably initiated ecological speciation and morphological diversification of this highly troglomorphic subterranean trechine genus.

Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal

The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.

The role of dispersal for shaping phylogeographical structure of flightless beetles from the Andes

Background

Páramo is a tropical alpine ecosystem present in the northern Andes. Its patchy distribution imposes limits and barriers to specialist inhabitants. We aim to assess the effects of this habitat distribution on divergence across two independently flightless ground beetle lineages, in the genera Dyscolus and Dercylus.

Methods

One nuclear and one mitochondrial gene from 110 individuals from 10 sites across the two lineages were sequenced and analyzed using a combination of phylogenetics, population genetic analyses, and niche modeling methods.

Results

The two lineages show different degrees of population subdivision. Low levels of gene flow were found in Dyscolus alpinus, where one dominant haplotype is found in four out of the six populations analyzed for both molecular markers. However, complete population isolation was revealed in species of the genus Dercylus, where high levels of differentiation exist at species and population level for both genes. Maximum entropy models of species in the Dercylus lineage show overlapping distributions. Still, species distributions appear to be restricted to small areas across the Andes.

Conclusion

Even though both beetle lineages are flightless, the dispersal ability of each beetle lineage appears to influence the genetic diversity across fragmented páramo populations, where Dyscolus alpinus appears to be a better disperser than species in the genus Dercylus.

Pleistocene climate change and the formation of regional species pools

Although the description of bioregions dates back to the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We used a network approach to identify regional and sub-regional faunas of European Carabus beetles and developed a method to explore the relative contribution of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at the Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events-such as Pleistocene climate cooling, rather than just deep-time evolutionary processes-can profoundly modify the composition and structure of geographical species pools.

The first stygobiont species of Coleoptera from Portugal, with a molecular phylogeny of the Siettitia group of genera (Dytiscidae, Hydroporinae, Hydroporini, Siettitiina)

Iberoporuspluto sp. n., the first stygobiont beetle from Portugal (Dytiscidae, Hydroporinae), is described from a single female from the cave Soprador do Carvalho (Coimbra). The species is highly troglomorphic, depigmented, blind, and with elongated appendages not adapted for swimming. A molecular phylogeny based on a combination of three mitochondrial and two nuclear genes showed the new species to be sister to I.cermenius Castro & Delgado, 2001 from Córdoba (south of Spain), within the subtribe Siettitiina of the tribe Hydroporini. Both species are included in a clade with Siettitiaavenionensis Guignot, 1925 (south of France) and Rhithrodytesagnus Foster, 1992 and R.argaensis Fery & Bilton, 1996 (north of Portugal), in turn sister to the rest of species of genus Rhithrodytes Bameul, 1989, in what is here considered the Siettitia group of genera. We resolve the paraphyly of Rhithrodytes by transferring the two Portuguese species to Iberoporus Castro & Delgado, 2001, I.agnus (Foster, 1992), comb. n. and I.argaensis (Fery & Bilton, 1996), comb. n.

Long-term population persistence of flightless weevils (Eurhoptus pyriformis) across old- and second-growth forests patches in southern Appalachia

Background

Southern Appalachian forests are dominated by second-growth vegetation following decades of intensive forestry and agricultural use, although some old-growth patches remain. While it’s been shown that second-growth areas may exhibit comparable species richness to old-growth in the area, the extent to which populations of arthropods in second-growth areas have persisted vs. recolonized from other areas remains unexamined. The implications for conservation of both classes of forest are significant. Here we analyze population diversity and relatedness across five old-growth and five second-growth populations of flightless, leaf litter-inhabiting beetles in the genus Eurhoptus (Coleoptera: Curculionidae: Cryptorhynchinae). Our main goal is asking whether second-growth areas show diminished diversity and/or signals of recolonization from old-growth sources.

Results

Population genetic and phylogenetic analyses do not reveal any consistent differences in diversity between the old-growth and second-growth populations examined. Some second-growth populations retain substantial genetic diversity, while some old-growth populations appear relatively depauperate. There is no phylogenetic indication that second-growth populations have recolonized from old-growth source populations.

Conclusions

Most populations contain substantial and unique genetic diversity indicating long-term persistence in the majority of sites. The results support substantial resilience in second-growth populations, though the geographic scale of sampling may have hindered detection of recolonization patterns. Broad scale phylogeographic patterns reveal a deep break across the French Broad River basin, as has been reported in several other taxa of limited dispersal abilities. In Eurhoptus this break dates to ~ 2–6 Ma ago, on the older end of the range of previously estimated dates.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1278-y) contains supplementary material, which is available to authorized users.

Hidden biodiversity: total evidence phylogenetics and evolution of morphological traits in a highly diverse lineage of endogean ground beetles, Typhlocharis Dieck, 1869 (Carabidae, Trechinae, Anillini)

Typhlocharis is the most diverse eyeless endogean ground beetle genus known to date, with 62 species all endemic to the West Mediterranean region. The lineage is characterized by a conservative and singular body plan within Carabidae that contrasts with a high morphological diversity in many traits. We provide an exhaustive phylogeny of the lineage through the study of 92 morphological characters from all 62 described species and 45 potential new species from 70 additional populations, and the combination of morphological and available molecular data, in the first total evidence phylogenetic approach for a highly diverse endogean lineage. We tracked the evolution of morphological traits over the obtained phylogenies. Results suggest eight morphologically distinct clades, which do not correspond to the species groups proposed formerly. Ancestral state reconstructions and phylogenetic signal analyses of morphological traits revealed that some of the previously key characters to the classification of Typhlocharis, such as the umbilicate series or the apical denticles of elytra, are highly homoplasic, whereas other characters show stronger phylogenetic signal, including structures in the antennae, gula, pronotum and last abdominal ventrite. This evidence supports the split of Typhlocharis into three genera: Lusotyphlus gen. nov.; Typhlocharis Dieck, 1869 and Microcharidius Coiffait, 1969 (revalidated), forming the subtribe Typhlocharina Jeanne, 1973.

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene-Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid-adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.

The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats.

The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing

The ongoing exploration of biodiversity and the implementation of new molecular tools continue to unveil hitherto unknown lineages. Here, we report the discovery of three species of neotenic beetles for which we propose the new family Iberobaeniidae. Complete mitochondrial genomes and rRNA genes recovered Iberobaeniidae as a deep branch in Elateroidea, as sister to Lycidae (net-winged beetles). Two species of the new genus Iberobaenia, Iberobaenia minuta sp. nov. and Iberobaenia lencinai sp. nov. were found in the adult stage. In a separate incidence, a related sequence was identified in bulk samples of soil invertebrates subjected to shotgun sequencing and mitogenome assembly, which was traced to a larval voucher specimen of a third species of Iberobaenia Iberobaenia shows characters shared with other elateroid neotenic lineages, including soft-bodiedness, the hypognathous head, reduced mouthparts with reduced labial palpomeres, and extremely small-bodied males without strengthening structures due to miniaturization. Molecular dating shows that Iberobaeniidae represents an ancient relict lineage originating in the Lower Jurassic, which possibly indicates a long history of neoteny, usually considered to be evolutionarily short-lived. The apparent endemism of Iberobaeniidae in the Mediterranean region highlights the importance of this biodiversity hotspot and the need for further species exploration even in the well-studied European continent.

Pleistocene range shifts, refugia and the origin of widespread species in western Palaearctic water beetles

Quaternary glacial cycles drove major shifts in both the extent and location of the geographical ranges of many organisms. During glacial maxima, large areas of central and northern Europe were inhospitable to temperate species, and these areas are generally assumed to have been recolonized during interglacials by range expansions from Mediterranean refugia. An alternative is that this recolonization was from non-Mediterranean refugia, in central Europe or western Asia, but data on the origin of widespread central and north European species remain fragmentary, especially for insects. We studied three widely distributed lineages of freshwater beetles (the Platambus maculatus complex, the Hydraena gracilis complex, and the genus Oreodytes), all restricted to running waters and including both narrowly distributed southern endemics and widespread European species, some with distributions spanning the Palearctic. Our main goal was to determine the role of the Pleistocene glaciations in shaping the diversification and current distribution of these lineages. We sequenced four mitochondrial and two nuclear genes in populations drawn from across the ranges of these taxa, and used Bayesian probabilities and Maximum Likelihood to reconstruct their phylogenetic relationships, age and geographical origin. Our results suggest that all extant species in these groups are of Pleistocene origin. In the H. gracilis complex, the widespread European H. gracilis has experienced a rapid, recent range expansion from northern Anatolia, to occupy almost the whole of Europe. However, in the other two groups widespread central and northern European taxa appear to originate from central Asia, rather than the Mediterranean. These widespread species of eastern origin typically have peripherally isolated forms in the southern Mediterranean peninsulas, which may be remnants of earlier expansion-diversification cycles or result from incipient isolation of populations during the most recent Holocene expansion. The accumulation of narrow endemics of such lineages in the Mediterranean may result from successive cycles of range expansion, with subsequent speciation (and local extinction in glaciated areas) through multiple Pleistocene climatic cycles.

Transoceanic origin of microendemic and flightless New Caledonian weevils

The origin of the astonishing New Caledonian biota continues to fuel a heated debate among advocates of a Gondwanan relict scenario and defenders of late oceanic dispersal. Here, we study the origin of New Caledonian Trigonopterus flightless weevils using a multimarker molecular phylogeny. We infer two independent clades of species found in the archipelago. Our dating estimates suggest a Late Miocene origin of both clades long after the re-emergence of New Caledonia about 37 Ma. The estimation of ancestral ranges supports an ancestral origin of the genus in a combined region encompassing Australia and New Guinea with subsequent colonizations of New Caledonia out of New Guinea in the mid-Miocene. The two New Caledonian lineages have had very different evolutionary trajectories. Colonizers belonging to a clade of foliage dwellers greatly diversified, whereas species inhabiting leaf-litter have been less successful.

The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes)

In most lineages, most species have restricted geographic ranges, with only few reaching widespread distributions. How these widespread species reached their current ranges is an intriguing biogeographic and evolutionary question, especially in groups known to be poor dispersers. We reconstructed the biogeographic and temporal origin of the widespread species in a lineage with particularly poor dispersal capabilities, the diving beetle genus Deronectes (Dytiscidae). Most of the ca. 60 described species of Deronectes have narrow ranges in the Mediterranean area, with only four species with widespread European distributions. We sequenced four mitochondrial and two nuclear genes of 297 specimens of 109 different populations covering the entire distribution of the four lineages of Deronectes, including widespread species. Using Bayesian probabilities with an a priori evolutionary rate, we performed (1) a global phylogeny/phylogeography to estimate the relationships of the main lineages within each group and root them, and (2) demographic analyses of the best population coalescent model for each species group, including a reconstruction of the geographical history estimated from the distribution of the sampled localities. We also selected 56 specimens to test for the presence of Wolbachia, a maternally transmitted parasite that can alter the patterns of mtDNA variability. All species of the four studied groups originated in the southern Mediterranean peninsulas and were estimated to be of Pleistocene origin. In three of the four widespread species, the central and northern European populations were nested within those in the northern areas of the Anatolian, Balkan and Iberian peninsulas respectively, suggesting a range expansion at the edge of the southern refugia. In the Mediterranean peninsulas the widespread European species were replaced by vicariant taxa of recent origin. The fourth species (D. moestus) was proven to be a composite of unrecognised lineages with more restricted distributions around the Western and Central Mediterranean. The analysis of Wolbachia showed a high prevalence of infection among Deronectes, especially in the D. aubei group, where all sequenced populations were infected with the only exception of the Cantabrian Mountains, the westernmost area of distribution of the lineage. In this group there was a phylogenetic incongruence between the mitochondrial and the nuclear sequence, although no clear pattern links this discordance to the Wolbachia infection. Our results suggest that, in different glacial cycles, populations that happened to be at the edge of the newly deglaciated areas took advantage of the optimal ecological conditions to expand their ranges to central and northern Europe. Once this favourable ecological window ended populations become isolated, resulting in the presence of closely related but distinct species in the Mediterranean peninsulas.