Smelling in the dark: Phylogenomic insights into the chemosensory system of a subterranean beetle

The chemosensory system has experienced relevant changes in subterranean animals, facilitating the perception of specific chemical signals critical to survival in their particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna has been largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to a deep subterranean environment) in order to investigate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odourant and gustatory gene repertoires compared to polyphagous beetles that inhabit surface habitats. Moreover, S. longicornis showed a large diversity of odourant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication of the ionotropic coreceptor IR25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may result from adaptation to the highly specific ecological niche it occupies, and that gene duplication and loss may have played an important role in the evolution of gene families involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level

The deep subterranean environment as a potential model system in ecological, biogeographical and evolutionary research

One of the main challenges in ecology, biogeography and evolution is to understand and predict how species may respond to environmental changes. Here we focus on the deep subterranean environment, a system that minimizes most of the typical uncertainties of studies on epigean (surface) environments. Caves are relatively homogeneous habitats with nearly constant environmental conditions and simplified biological communities, allowing to control for biotic interactions. Thus, this particular system could be considered a natural habitat whose environmental conditions are similar to what can be reproduced in a laboratory, being an ideal model system for ecological, biogeographical and evolutionary studies. Subterranean species may potentially be used to assess the capability to persist in situ in a global change scenario, as they cannot accommodate to drastic changing conditions by behavioural plasticity, microhabitat use or by migrating to distant, more suitable areas, something frequent in epigean environments. In order to provide accurate predictions of the response of the subterranean biodiversity to climate change, we encourage evolutionary biologist, biogeographers and conservation biologist to work in this interesting ecosystem.DS-F was supported by a post-doctoral contract funded by Universidad de Castilla-La Mancha and the European Social Fund (ESF). This work was partly funded by two projects funded by the Spanish Ministry of Economy and Competitiveness (CGL2016-76995-P to DSF and CGL2016-76705-P to IR).Peer reviewe

Thermal niche evolution and geographical range expansion in a species complex of western Mediterranean diving beetles

[Background] Species thermal requirements are one of the principal determinants of their ecology and biogeography, although our understanding of the interplay between these factors is limited by the paucity of integrative empirical studies. Here we use empirically collected thermal tolerance data in combination with molecular phylogenetics/phylogeography and ecological niche modelling to study the evolution of a clade of three western Mediterranean diving beetles, the Agabus brunneus complex.[Results] The preferred mitochondrial DNA topology recovered A. ramblae (North Africa, east Iberia and Balearic islands) as paraphyletic, with A. brunneus (widespread in the southwestern Mediterranean) and A. rufulus (Corsica and Sardinia) nested within it, with an estimated origin between 0.60-0.25 Ma. All three species were, however, recovered as monophyletic using nuclear DNA markers. A Bayesian skyline plot suggested demographic expansion in the clade at the onset of the last glacial cycle. The species thermal tolerances differ significantly, with A. brunneus able to tolerate lower temperatures than the other taxa. The climatic niche of the three species also differs, with A. ramblae occupying more arid and seasonal areas, with a higher minimum temperature in the coldest month. The estimated potential distribution for both A. brunneus and A. ramblae was most restricted in the last interglacial, becoming increasingly wider through the last glacial and the Holocene.[Conclusions] The A. brunneus complex diversified in the late Pleistocene, most likely in south Iberia after colonization from Morocco. Insular forms did not differentiate substantially in morphology or ecology, but A. brunneus evolved a wider tolerance to cold, which appeared to have facilitated its geographic expansion. Both A. brunneus and A. ramblae expanded their ranges during the last glacial, although they have not occupied areas beyond their LGM potential distribution except for isolated populations of A. brunneus in France and England. On the islands and possibly Tunisia secondary contact between A. brunneus and A. ramblae or A. rufulus has resulted in introgression. Our work highlights the complex dynamics of speciation and range expansions within southern areas during the last glacial cycle, and points to the often neglected role of North Africa as a source of European biodiversity.This work was supported by an FPI grant to AH-G and projects CGL2007-61665 and CGL2010-15755 from the Spanish government to IR. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe

Applications of proteomics in ecology and evolution

La evolución de las características ecológicas de las especies es uno de los temas más intensamente estudiados, pero su complejidad suele limitar estos estudios a evidencias indirectas de las adaptaciones reales de los organismos. Recientemente, métodos moleculares como los "micro-arrays" y la secuenciación a gran escala han incrementado de manera notable el conocimiento de los genomas y las vías metabólicas. Con ello, ha sido posible por primera vez estudiar con detalle la interacción a nivel molecular de los organismos con su medio. Sin embargo, la investigación de los procesos bioquímicos asociados a cuestiones ecológicas y evolutivas relacionando a los organismos con sus hábitats se suele limitar a los llamados "organismos modelo". Los últimos avances en proteómica han permitido un enorme incremento de su uso en ecología y biología evolutiva. Estas metodologías son en muchos aspectos perfectamente aplicables a estudios ecológicos, ofreciendo la posibilidad de trabajar con una amplia gama de organismos. En este trabajo hacemos una breve revisión de las principales metodologías y de cómo la proteómica se ha utilizado hasta la fecha en diferentes estudios ecológicos y evolutivos en organismos no-modelo.The evolution of ecological traits has been subject to intense research efforts for a long time. The complexity of ecological traits usually limits these studies to indirect evidence on the actual adaptive variations. More recently, molecular methods, such as micro-arrays and large-scale genomic sequencing, considerably increased the knowledge on genomes and metabolic pathways. With this, it became possible for the first time to study in detail the interaction of organisms and their environment at the molecular level. However, the investigation of biochemical processes associated to ecological and evolutionary questions relating organisms to their habitats are typically restricted to so-called model organisms. The latest methodological advances in proteomics led to a strongly increase in their use in ecology and evolutionary biology. These approaches are in many respects suitable for ecological studies, and offer the possibility to work on a wide range of organisms. Here we briefly review the methodology and describe how proteomics has been used to date in different fields of evolutionary biology and ecology in non-model organisms.Proyectos CGL2007-61943 y CGL2007-61665

Life-history specialization was not an evolutionary dead-end in Pyrenean cave beetles

Research on subterranean organisms has focused on the colonization process and some of the associated phenotypic changes, but little is known on the long-term evolutionary dynamics of subterranean lineages and the origin of some highly specialized complex characters. One of the most extreme modifications is the reduction of the number of larval instars in some Leptodirini beetles from the ancestral 3 to 2 and ultimately a single instar. This reduction is usually assumed to have occurred independently multiple times within the same lineage and geographical area, but its evolution has never been studied in a phylogenetic framework. Using a comprehensive molecular phylogeny, we found a low number of independent origins of the reduction in the number of instars, with a single transition, dated to the Oligocene-Miocene, from 3 to 2 and then 1 instar in the Pyrenees, the best-studied area. In the Pyrenees, the 1-instar lineage had a diversification rate (0.22 diversification events per lineage per million years) significantly higher than that of 3- or 2-instar lineages (0.10), and similar to that seen in other Coleopteran radiations. Far from being evolutionary dead-ends, ancient lineages fully adapted to subterranean life seem able to persist and diversify over long evolutionary periods. © 2014 The Author(s) Published by the Royal Society. All rights reserved.This work was funded by projects CGL2007-61943 and CGL2006-11403 from the Ministerio de Ciencia e Innovación (MICINN, Spain) to A.C.Peer Reviewe

Developmental constraints in cave beetles

In insects, whilst variations in life cycles are common, the basic patterns typical for particular groups remain generally conserved. One of the more extreme modifications is found in some subterranean beetles of the tribe Leptodirini, in which the number of larval instars is reduced from the ancestral three to two and ultimately one, which is not active and does not feed. We analysed all available data on the duration and size of the different developmental stages and compared them in a phylogenetic context. The total duration of development was found to be strongly conserved, irrespective of geographical location, habitat type, number of instars and feeding behaviour of the larvae, with a single alteration of the developmental pattern in a clade of cave species in southeast France. We also found a strong correlation of the size of the first instar larva with adult size, again regardless of geographical location, ecology and type of life cycle. Both results suggest the presence of deeply conserved constraints in the timing and energy requirements of larval development. Past focus on more apparent changes, such as the number of larval instars, may mask more deeply conserved ontogenetic patterns in developmental timing. © 2014 The Author(s) Published by the Royal Society.This work was partially funded by the Spanish Government project nos. CGL2007-61943 and CGL2006-11403 to A.C.Peer Reviewe

Aquatic coleoptera of north oman, with description of new species of hydraenidae and hydrophilidae

We report the aquatic Coleoptera (families Dryopidae, Dytiscidae, Georissidae, Gyrinidae, Heteroceridae, Hydraenidae, Hydrophilidae and Limnichidae) from North Oman, mostly based on the captures of fourteen localities sampled by the authors in 2010. Four species are described as new, all from the Al Hajar mountains, three in family Hydraenidae, Hydraena (Hydraena) naja sp. nov., Ochthebius (Ochthebius) alhajarensis sp. nov. (O. punc-tatus species group) and O. (O.) bernard sp. nov. (O. metallescens species group); and one in family Hydrophilidae, Agraphydrus elongatus sp. nov. Three of the recorded species are new to the Arabian Peninsula, Hydroglyphus farquharensis (Scott, 1912) (Dytiscidae), Hydraena (Hydraenopsis) quadricollis Wollaston, 1864 (Hydraenidae) and Enochrus (Lumetus) cf. quadrinotatus (Guillebeau, 1896) (Hydrophilidae). Ten species already known from the Arabian Peninsula are newly recorded from Oman: Cybister tripunctatus lateralis (Fabricius, 1798) (Dytiscidae), Hydraena (Hydraena) gattolliati Jäch & Delgado, 2010, Ochthebius (Ochthebius) monseti Jäch & Delgado 2010, Ochthebius (Ochthebius) wurayah Jäch & Delgado, 2010 (all Hydraenidae), Georissus (Neogeorissus) chameleo Fikáček & Trávníček, 2009 (Georissidae), Enochrus (Methydrus) cf. tetraspilus Régimbart, 1903, Laccobius (Hydroxenus) leucaspis Kiesenwetter, 1870, Paracymus relaxus Rey, 1884 (all Hydrophilidae), Dryops lutulentus (Erichson, 1947) (Dryopidae), and Augyles flavidus (Rossi, 1794) (Heteroceridae). A total of 73 species of aquatic Coleoptera are presently known from Oman, although this number is expected to increase substantially with further sampling. A checklist of the species of aquatic Coleoptera from the Arabian Peninsula is provided.We also thank Rocío Alonso and Anabela Cardoso (IBE) for laboratory work, and funding from projects CGL2007-61665, CGL2013-48950-C2-1-P and CGL2016-76705-P (AEI/FEDER, UE)

Thermal niche estimators and the capability of poor dispersal species to cope with climate change

For management strategies in the context of global warming, accurate predictions of species response are mandatory. However, to date most predictions are based on niche (bioclimatic) models that usually overlook biotic interactions, behavioral adjustments or adaptive evolution, and assume that species can disperse freely without constraints. The deep subterranean environment minimises these uncertainties, as it is simple, homogeneous and with constant environmental conditions. It is thus an ideal model system to study the effect of global change in species with poor dispersal capabilities. We assess the potential fate of a lineage of troglobitic beetles under global change predictions using different approaches to estimate their thermal niche: bioclimatic models, rates of thermal niche change estimated from a molecular phylogeny, and data from physiological studies. Using bioclimatic models, at most 60% of the species were predicted to have suitable conditions in 2080. Considering the rates of thermal niche change did not improve this prediction. However, physiological data suggest that subterranean species have a broad thermal tolerance, allowing them to stand temperatures never experienced through their evolutionary history. These results stress the need of experimental approaches to assess the capability of poor dispersal species to cope with temperatures outside those they currently experience.DSF was supported by a “Juan de la Cierva” postdoctoral contract from the Spanish Ministry of Economy and Competitiveness and another post-doctoral contract funded by Universidad de Castilla-La Mancha and the European Social Fund (ESF).This work was partly funded by project (DFG FA 1042/1-1) to AF and CGL2010-15755 to I.R.Peer reviewe

Filogeografía del grupo Agabus brunneus (Dytiscidae: Coleoptera): evaluando/resolviendo una especiación reciente

Trabajo presentado en el I Congreso Ibérico de Sistemática Animal (CISA2012), celebrado en Madrid del 17 al 19 de enero de 2012.El grupo de especies de Agabus brunneus (Dytiscidae: Coleoptera) está compuesto de tres especies que presentan unos rangos de distribución muy distintos. Dos de ellas tienen un rango reducido (Agabus ramblae Millán y Ribera, 2001 en el SE Ibérico y Marruecos y Agabus rufulus Fairmaire, 1859 en Córcega y Cerdeña) mientras que la tercera se distribuye en gran parte de Europa y Norte de África (Agabus brunneus (Fabricius, 1798)). La diversificación en este grupo de especies es muy reciente, de manera que los marcadores mitocondriales empleados (cox1 y rrnL) no presentan suficiente variación para resolver la filogeografía del grupo. Evaluamos en este trabajo la capacidad de otro marcador (proteína de función desconocida) desarrollada para otra familia de coleópteros (Leiodidae) que presenta una variabilidad comparable a la del gen cox1. La separación inicial de estas tres especies se realizó en base a caracteres morfológicos del edeago y la morfología externa. Presentamos también un análisis morfométrico de varios caracteres del individuo y del edeago para confirmar esta separación.Peer reviewe

Reproducibility and consistency of proteomic experiments on natural populations of a nonmodel aquatic insect species

Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2–3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.This work was funded by the Spanish government through the I+D+i programme, grants CGL2007-61665 and CGL2010-15755.Peer Reviewe