A molecular phylogeny shows the single origin of the Pyrenean subterranean Trechini ground beetles (Coleoptera: Carabidae)

A Case for Below-Ground Dispersal? Insights into the Biology, Ecology and Conservation of Blind Cave Spiders in the Genus Troglodiplura (Mygalomorphae: Anamidae)

Previously described from only fragments of exoskeleton and juvenile specimens, the cave spider genus Troglodiplura (Araneae: Anamidae), endemic to the Nullarbor Plain, is the only troglomorphic member of the infraorder Mygalomorphae recorded from Australia. We investigated the distribution of Troglodiplura in South Australia, collecting and observing the first (intact) mature specimens, widening the number of caves it has been recorded in, and documenting threats to conservation. Phylogenetic analyses support the placement of Troglodiplura as an independent lineage within the subfamily Anaminae (the 'Troglodiplura group') and provide unequivocal evidence that populations from apparently isolated cave systems are conspecifics of T. beirutpakbarai Harvey & Rix, 2020, with extremely low or negligible inter-population mitochondrial divergences. This is intriguing evidence for recent or contemporary subterranean dispersal of these large, troglomorphic spiders. Observations of adults and juvenile spiders taken in the natural cave environment, and supported by observations in captivity, revealed the use of crevices within caves as shelters, but no evidence of silk use for burrow construction, contrasting with the typical burrowing behaviours seen in other Anamidae. We identify a range of threats posed to the species and to the fragile cave ecosystem, and provide recommendations for further research to better define the distribution of vulnerable taxa within caves and identify actions needed to protect them.

Morphological Adaptation of Cave-Dwelling Ground Beetles in China Revealed by Geometric Morphometry (Coleoptera, Carabidae, Trechini)

Simple Summary

Cavernicolous ground beetles dwelling in China are one of the most diverse and underground-adapted coleopteran group in the world. The tribe Trechini is, among them, the most representative group constituting over 170 known species with a narrow and elongated body and long appendages or a stout body and short appendages. However, very little information about their morphology has been explored. The aim of this study was to analyze the morphological adaptations of this group using geometric morphological methods. The beetles were divided into four different morphological types, including aphaenopsian, semi-aphaenopsian, anophthalmic, and surface-dwelling, and the analysis is based on the morphology of their head, pronotum, and elytra. Our findings indicate that the overall morphological variation of cave trechine beetles has gradually specialized from an anophthalmic to semi-aphaenopsian to aphaenopsian type. Different types have different directions of variation in the head, pronotum, and elytra, but the pronotum is more differentiated and morphologically diverse than the head and elytra.

Abstract

Cave-dwelling ground beetles in China represent the most impressive specific diversity and morphological adaptations of the cavernicolous ground beetles in the world, but they have not been systematically examined in quantitative terms. The present study focuses on the application of geometric morphological methods to address the morphological adaptations of the tribe Trechini, the most representative group in China. We have employed a geometric morphometry analysis of the head, pronotum, and elytra of 53 genera of Trechini, including 132 hypogean and 8 epigean species. Our results showed that the overall morphological variation of cave carabids has gradually specialized from an anophthalmic to semi-aphaenopsian to aphaenopsian type. There were extremely significant differences (p < 0.01) among four different adaptive types including aphaenopsian, semi-aphaenopsian, anophthalmic, and surface-dwelling Trechini when their adaptability to a cave environment was used as the basis for grouping. Furthermore, there were differences in the phenotypic tree of the head, pronotum, and elytra, and an integrated morphology. To the best of our knowledge, this is the first report on the analysis of the head, pronotum, and elytra of four different adaptive types of ground beetles in order to clarify the morphological adaptations of cavernicolous carabids to the cave environment.

Global Diversification of Anelosimus Spiders Driven by Long-Distance Overwater Dispersal and Neogene Climate Oscillations

Vicariance and dispersal events, combined with intricate global climatic history, have left an imprint on the spatiotemporal distribution and diversity of many organisms. Anelosimus cobweb spiders (Theridiidae), are organisms ranging in behavior from solitary to highly social, with a cosmopolitan distribution in temperate to tropical areas. Their evolutionary history and the discontinuous distribution of species richness suggest that 1) long-distance overwater dispersal and 2) climate change during the Neogene (23-2.6 Ma), may be major factors in explaining their distribution and diversification. Here, we test these hypotheses, and explicitly test if global Miocene/Pliocene climatic cooling in the last 8 Ma affected Anelosimus radiation in parallel in South America and Madagascar. To do so, we investigate the phylogeny and spatiotemporal biogeography of Anelosimus through a culmination of a 20-year comprehensive global sampling at the species level (69 species, including 84% of the known 75 species worldwide, represented by 268 individuals) using nucleotide data from seven loci (5.5 kb). Our results strongly support the monophyly of Anelosimus with an Oligocene ($\sim $30 Ma) South American origin. Major clades on other continents originate via multiple, long-distance dispersal events, of solitary or subsocial-but not social-lineages, from the Americas. These intercontinental dispersals were to Africa, Madagascar (twice), and SE Asia/Australasia. The early diversification of Anelosimus spiders coincides with a sudden thermal increase in the late Oligocene ($\sim $27-25 Ma), though no causal connection can be made. Our results, however, strongly support the hypothesis that global Neogene climatic cooling in the last 8 Ma drove Anelosimus radiation in parallel in South America and Madagascar, offering a rare empirical evidence for diversification of a socially diverse group driven by an interplay between long-distance dispersal and global Neogene climatic changes. [Cobweb spiders; diversification; global biogeography; long-distance dispersal; molecular phylogenetics; neogene climate changes; sociality; vicariance.].

Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago

Most subterranean animals are assumed to have evolved from surface ancestors following colonization of a cave system; however, very few studies have raised the possibility of "subterranean speciation" in underground habitats (i.e., obligate cave-dwelling organisms [troglobionts] descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raise the possibility of subterranean speciation. We tested this hypothesis using vision (phototransduction) genes that are evolving under neutral processes in subterranean species and purifying selection in surface species. Using sequence data from 32 subterranean and five surface species in the genus Paroster (Dytiscidae), we identified deleterious mutations in long wavelength opsin (lwop), arrestin 1 (arr1), and arrestin 2 (arr2) shared by a sympatric sister-species triplet, arr1 shared by a sympatric sister-species pair, and lwop and arr2 shared among closely related species in adjacent calcrete aquifers. In all cases, a common ancestor possessed the function-altering mutations, implying they were already adapted to aphotic environments. Our study represents one of the first confirmed cases of subterranean speciation in cave insects. The assessment of genes undergoing pseudogenization provides a novel way of testing modes of speciation and the history of diversification in blind cave animals.

Unexpected Species Identities and Interspecific Relationships in a Subterranean Beetle Lineage, the Pterostichus macrogenys Species Group (Coleoptera, Carabidae), Revealed by Fine-Scale Field Sampling and Detailed Morphological Comparisons

An endemic subterranean Japanese carabid beetle lineage, the Pterostichus macrogenys species group, was recently revealed to have marked regional differentiation. Studies of such features reveal insect species diversity and provide insight into the mechanisms driving species diversity. We examined specimens of this species group collected from the southern Tohoku District of Honshu, Japan, where its diversity has not yet been fully elucidated, using fine-scale field sampling and detailed comparative morphological analysis of male genitalia. In total, 103 specimens from 13 localities were classified into one new (P. monolineatus sp. n.) and eight known species. In four of the known species, we observed disjunct distributions, which have not previously been reported in this species group and may be more common than previously recognized. Species coexistence was observed at four sites, with two species of different body sizes coexisting at three sites and three species coexisting at the remaining site. The three coexisting species included one large and two small species, the latter of which have male genitalia of a different size. This newly discovered coexistence pattern implies separate effects of differential body and genital size in species coexistence, which has rarely been reported in insects.

Towards an evolutionary history of European-Alpine Trechus ground beetles: Species groups and wing reduction

The evolution of flight triggered the rise of pterygote insects, but secondary flightlessness has evolved numerous times and is often associated with reduced gene flow among populations and patterns of diversification. With 85 species most of which are wing reduced, the ground beetle genus Trechus in the European Alps may be one such example. Here, we reconstructed a molecular phylogeny using 72 of these species based on mitochondrial and nuclear DNA sequences as a basis for reconstructing their evolutionary history. We rearranged the species into 20 monophyletic species groups, of which five are novel and 15 were already established but with different species allocated. Wing measurements revealed a strong tendency for wing reduction but also variation within and among species, with the few fully-winged species distributed across multiple species groups containing also wing-reduced species. Using character mapping and phylogenetic independent contrasts, we found that neither distribution area, body size, pigmentation, elevational zone, nor hygrophily explained wing status in our sample. Assessing five completely sampled clades, we inferred that each of their ancestors had most likely already been wing reduced. We discuss putative scenarios explaining this pattern and the presence of wing polymorphism across the phylogeny. One plausible scenario would be an already wing-reduced last common ancestor of all Trechus species and multiple regains of full wing length via back mutation and/or hybridisation. Alternatively and possibly more likely, the ancestors were either fully winged, with subsequent rapid and repeated wing reduction explaining the current wing-status pattern, or polymorphic, with long-term polymorphism or reselection acting on standing genetic variation explaining the recent fully-winged species. Either way, Trechus ground beetles are a promising, taxonomically and ecologically diverse system for studying the evolution of flightlessness. Areas for future research include morphological assessment of flight muscles, functional analysis of flight capability, and exploration of the mechanistic and genetic bases of wing and flight evolution.

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.

Too hot to handle: Cenozoic aridification drives multiple independent incursions of Schizomida (Hubbardiidae) into hypogean environments

The formation of the Australian arid zone, Australia's largest and youngest major biome, has been recognized as a major driver of rapid evolutionary radiations in terrestrial plants and animals. Here, we investigate the phylogenetic diversity and evolutionary history of subterranean short-tailed whip scorpions (Schizomida: Hubbardiidae), which are a significant faunal component of Western Australian hypogean ecosystems. We sequenced two mitochondrial (12S, COI) and three nuclear DNA markers (18S, 28S, ITS2) from ∼600 specimens, largely from the genera Draculoides and Paradraculoides, including 20 previously named species and an additional 56 newly identified operational taxonomic units (OTUs). Phylogenetic analyses revealed a large and rapid species radiation congruent with Cenozoic aridification of the continent, in addition to the identification of a new genus in Western Australia and the first epigean schizomid from the Pilbara. Here, we also synonymise Paradraculoides with Draculoides (new synonymy), due to paraphyly and a lack of reliable characters to define the two genera. Our results are consistent with multiple colonisations of the subterranean realm from epigean ancestors as their forest habitat fragmented and retracted, with ongoing fragmentation and diversification of lineages underground. These findings illustrate the remarkable diversity and high incidence of short-range endemism of Western Australia's subterranean fauna, which has important implications for identifying and managing short-range endemic subterranean fauna. They also highlight the advantages of including molecular data in subterranean fauna surveys as all specimens can be utilized, regardless of sex and life stage. Additionally, we have provided the first multi-gene phylogenetic framework for Australian schizomids, which will enable researchers and environmental consultants to identify new taxa or align them to existing lineages.

Mitochondrial sequence data indicate “Vicariance by Erosion” as a mechanism of species diversification in North American Ptomaphagus (Coleoptera, Leiodidae, Cholevinae) cave beetles

Small carrion beetles (Coleoptera: Leiodidae: Cholevinae) are members of cave communities around the world and important models for understanding the colonization of caves, adaptation to cave life, and the diversification of cave-adapted lineages. We developed a molecular phylogeny to examine the diversification of the hirtus-group of the small carrion beetle genus Ptomaphagus. The hirtus-group has no surface-dwelling members; it consists of 19 short-range endemic cave- and soil-dwelling species in the central and southeastern United States of America. Taxonomic, phylogenetic and biogeographic data were previously interpreted to suggest the hirtus-group diversified within the past 350,000 years through a series of cave colonization and speciation events related to Pleistocene climate fluctuations. However, our time-calibrated molecular phylogeny resulting from the analysis of 2,300 nucleotides from five genes across three mitochondrial regions (cox1, cytb, rrnL-trnL-nad1) for all members of the clade paints a different picture. We identify three stages of diversification in the hirtus-group: (1) ~10 million years ago (mya), the lineage that develops into P.shapardi, a soil-dwelling species from the Ozarks, diverged from the lineage that gives rise to the 18 cave-obligate members of the group; (2) between 8.5 mya and 6 mya, seven geographically distinct lineages diverged across Kentucky, Tennessee, Alabama and Georgia; six of these lineages represent a single species today, whereas (3) the ‘South Cumberlands’ lineage in Tennessee and Alabama diversified into 12 species over the past ~6 my. While the events triggering diversification during the first two stages remain to be determined, the distributions, phylogenetic relationships and divergence times in the South Cumberlands lineage are consistent with populations being isolated by vicariant events as the southern Cumberland Plateau eroded and fragmented over millions of years.

Phylogeny of the beetle supertribe Trechitae (Coleoptera: Carabidae): Unexpected clades, isolated lineages, and morphological convergence

Using data from two nuclear ribosomal genes and four nuclear protein-coding genes, we infer a well-resolved phylogeny of major lineages of the carabid beetle supertribe Trechitae, based upon a sampling of 259 species. Patrobini is the sister group of Trechitae, but the genus Lissopogonus appears to be outside of the Patrobini + Trechitae clade. We find that four enigmatic trechite genera from the Southern Hemisphere, Bembidarenas, Argentinatachoides, Andinodontis, and Tasmanitachoides, form a clade that is the sister group of Trechini; we describe this clade as a new tribe, Bembidarenini. Bembidarenini + Trechini form the sister group of remaining trechites. Within Trechini, subtribe Trechodina is not monophyletic, as three trechodine genera from Australia (Trechobembix, Paratrechodes, Cyphotrechodes) are the sister group of subtribe Trechina. Trechini appears to have originated in the continents of the Southern Hemisphere, with almost all Northern Hemisphere lineages representing a single radiation within the subtribe Trechina. We present moderate evidence that the geographically and phylogenetically isolated genera Sinozolus (six species in the mountains of China), Chaltenia (one species in Argentina and Chile), and Phrypeus (one species in western North America) also form a clade, the tribe Sinozolini. The traditionally recognized tribe Bembidiini sens. lat., diagnosed by the presence of a subulate terminal palpomere, is shown to be polyphyletic; subulate palpomeres have arisen five times within Trechitae. Anillini is monophyletic, and the sister group of Tachyini + Pogonini + Bembidiini + Zolini + Sinozolini; within anillines, we confirm earlier results indicating the eyed New Zealand genus Nesamblyops as the sister to the rest. Sampled New World Pogonini are monophyletic, rendering the genus Pogonus non-monophyletic. Tachyina and Xystosomina are sister groups. Within Xystosomina, the New World members are monophyletic, and are sister to an Australia-New Zealand clade. The latter consists of the genus Philipis as well as taxa not previously recognized as xystosomines: Kiwitachys, the "Tachys" ectromioides group, and "Tachys" mulwalensis. Within Tachyina, the subgenus Elaphropus is not closely related to other subgenera previously placed in the genus Elaphropus; we move the other subgenera into the genus Tachyura. Tachyina with a bifoveate mentum do not form a clade; in fact, a bifoveate mentum is found in Xystosomina, Sinozolini, Trechini, Trechitae and its sister group, Patrobini. Extensive homoplasy in the morphological characters previously used as key indicators of relationship is supported by our results: in addition to multiple origins of subulate palpomeres and bifoveate menta, a concave protibial notch has arisen independently in Anillina, Xystosomina, and Tachyina. Phylogenetically and geographically isolated, species-poor lineages in Trechini, Bembidarenini, and Sinozolini may be relicts of more widespread faunas; many of these are found today on gravel or sand shores of creeks and rivers, which may be an ancestral habitat for portions of Trechitae. In addition to the description of Bembidarenini, we present a diagnosis of the newly delimited Sinozolini, and keys to the tribes of Trechitae.

The thoracic morphology of cave-dwelling and free-living ground beetles from China (Coleoptera, Carabidae, Trechinae)

External and internal thoracic structures of two carabid species (Trechini) were examined and documented with different techniques. The study has a main focus on the eyeless cave-dwelling specialist Sinaphaenops wangorum, but detailed information is also provided for a species occurring in cave entrances. The phylogenetic background of the structural features of the thoracic skeletomuscular system was addressed. The thoracic morphology of the examined species was compared to conditions observed in previously studied carabids and non-related subterranean leiodids (Staphylinoidea) in order to identify cave adaptations. Main thoracic character complexes linked with cavernicolous habits in Trechini are elongation of the pro- and mesothorax and the legs, and a complete and irreversible reduction of the flight apparatus. The lost flight capacity is linked with a far reaching modification of skeletal elements of the metathorax including a strongly shortened and simplified metanotum, a shortened metaventrite, and completely reduced wings and sclerites of the wing base. The elongate prothorax together with the long and slender head and elongated legs distinctly increases the activity range in the subterranean lightless environment, which likely facilitates foraging of the carnivorous beetles. Some of the observed features like wing loss and elongation of the anterior thorax and legs are also found in some cave-dwelling Leiodidae (Leptodirini), whereas some other subterranean members of the staphylinoid family have a compact body and legs of normal length. In contrast to the predaceous Trechini, Leptodirini are scavengers.

Comprehensive evolutionary analysis of the Anthroherpon radiation (Coleoptera, Leiodidae, Leptodirini)

The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.

Diversification in tropics and subtropics following the mid-Miocene climate change: A case study of the spider genus Nesticella

Caves may offer suitable refugia for troglophilic invertebrates during periods of unfavourable climatic conditions because of their stable microclimates. As a consequence, allopatric divergence from their epigean counterparts may occur, leading to formation of truly hypogean communities (the Climatic Relict Hypothesis). Unlike the well-studied effects of Pleistocene glaciations, we know little about how ancient climate changes drove the development of cave-dwelling organisms living at both middle and lower latitudes. We investigate the evolutionary history of the troglophilic spider genus Nesticella (Araneae, Nesticidae) in relation to Asian Neogene (23-2.6 Ma) climatic changes. Our analyses discern clear differences in the evolution of the two main clades of Nesticella, which occur in temperate/subtropical and tropical latitudes. Eastern Asian Nesticella gradually evolved greater sedentariness and a strict subterranean lifestyle starting from the middle Miocene Epoch (~15-14 Ma) in conjunction with the progressive deterioration of the climate and vegetational shifts. Caves appear to have acted as refugia because of their internally uniform temperature and humidity, which allowed these spiders to survive increasing external seasonality and habitat loss. In contrast, a uniform accumulation of lineages, long-lasting times for dispersals and the lack of a comparable habitat shifting characterized the tropical lineage. This difference in pattern likely owes to the mild effects of climate change at low latitudes and the consequent lack of strong climatic drivers in tropical environments. Thus, the mid-Miocene climatic shift appears to be the major evolutionary force shaping the ecological differences between Asian troglophilic invertebrates and the driver of the permanent hypogean communities in middle latitudes.

X-ray microscopy reveals endophallic structures in a new species of the ground beetle genus Trechus Clairville, 1806 from Baltic amber (Coleoptera, Carabidae, Trechini)

The third fossil species of the genus Trechus Clairville, 1806 is described from Baltic amber: Trechusexhibitoriussp. n. Details of external and internal morphology were analysed using X-ray micro-computed tomography (micro-CT) and important diagnostic features of the internal male genital sac (endophallus) are described in detail for the first time in a fossil ground beetle. Based on these data, we could assign Trechusexhibitoriussp. n. to Trechus sensu stricto and this new fossil species seems to represent a basal branch of a lineage comprising species diverse groups of extant Trechus mainly distributed in the Caucasus and Anatolia. Thus, our results support previous studies suggesting that Trechus is a phylogenetically old lineage already present in the Eocene with numerous species.

Alpine endemic spiders shed light on the origin and evolution of subterranean species

We designed a comparative study to unravel the phylogeography of two Alpine endemic spiders characterized by a different degree of adaptation to subterranean life: Troglohyphantes vignai (Araneae, Linyphiidae) and Pimoa rupicola (Araneae, Pimoidae), the latter showing minor adaptation to hypogean life. We sampled populations of the model species in caves and other subterranean habitats across their known geographical range in the Western Alps. By combining phylogeographic inferences and Ecological Niche Modeling techniques, we inferred the biogeographic scenario that led to the present day population structure of the two species. According to our divergent time estimates and relative uncertainties, the isolation of T. vignai and P. rupicola from their northern sister groups was tracked back to Middle–Late Miocene. Furthermore, the fingerprint left by Pleistocene glaciations on the population structure revealed by the genetic data, led to the hypothesis that a progressive adaptation to subterranean habitats occurred in T. vignai, followed by strong population isolation. On the other hand, P. rupicola underwent a remarkable genetic bottleneck during the Pleistocene glaciations, that shaped its present population structure. It seems likely that such shallow population structure is both the result of the minor degree of specialization to hypogean life and the higher dispersal ability characterizing this species. The simultaneous study of overlapping spider species showing different levels of adaptation to hypogean life, disclosed a new way to clarify patterns of biological diversification and to understand the effects of past climatic shift on the subterranean biodiversity.

Convergent Reduction of Ovariole Number Associated with Subterranean Life in Beetles

BACKGROUND

Some species of obligate cavernicolous beetles are known to possess a unique feature-a contraction of the larval cycle. In contrast to many other subterranean beetles, life-cycle contraction in Trechini ground beetles (Carabidae) is correlated with a reduction in the number of eggs and a drastic reduction in the number of ovarioles. This remarkable peculiarity has only been reported for a small number of closely related species.

RESULTS

We give a description of the female internal reproductive system for six species of Trechini, including five subterranean species, with a particular focus on the western Pyrenean radiation of Aphaenops, a group for which nothing is known regarding the early life stages. We redescribe the internal female genitalia of A. crypticola Linder. Study of the ovarioles allowed us to infer the postembryonic development of the larvae for each species examined. We then used a phylogenetic framework to recognize two independent reductions in the number of ovarioles in the Pyrenean lineage. We discuss the multiple convergent evolutions in ovariole number and the potential link between a reduction of ovariole number and troglobiomorphism in a phylogenetic context.

CONCLUSIONS

There is an extreme reduction in ovariole number and size within the species studied; the eggs produced by small ovarioles have a remarkably large size. A reduction to one ovariole has occurred independently at least twice in this subterranean group. A reduction in the number of ovarioles in ground beetles is one of the striking consequences of subterranean specialization and it is correlated with another remarkable adaptation of subterranean beetles, a reduction in the number of larval instars.

Lack of evolutionary adjustment to ambient temperature in highly specialized cave beetles

Background

A key question in evolutionary biology is the relationship between species traits and their habitats. Caves offer an ideal model to test the adjustment of species to their surrounding temperature, as they provide homogeneous and simple environments. We compared two species living under different thermal conditions within a lineage of Pyrenean beetles highly modified for the subterranean life since the Miocene. One, Troglocharinus fonti, is found in caves at 4-11°C in the ancestral Pyrenean range. The second, T. ferreri, inhabits the coastal area of Catalonia since the early Pliocene, and lives at 14-16°C.

Results

We found no differences in their short term upper thermal limit (ca. 50°C), similar to that of most organisms, or their lower thermal limit (ca. -2.5°C), higher than for most temperate insects and suggesting the absence of cryoprotectants. In longer term tests (7 days) survival between 6-20°C was almost 100% for both species plus two outgroups of the same lineage, but all four died between 23-25°C, without significant differences between them.

Conclusions

Our results suggest that species in this lineage have lost some of the thermoregulatory mechanisms common in temperate insects, as their inferred default tolerance range is larger than the thermal variation experienced through their whole evolutionary history.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0288-2) contains supplementary material, which is available to authorized users.

Du'an Karst of Guangxi: a kingdom of the cavernicolous genus Dongodytes Deuve (Coleoptera, Carabidae, Trechinae)

Recent cave biodiversity surveys carried out in Du'an County and its adjacent areas of northwestern Guangxi, China, have revealed some exciting scientific findings. In a very limited area seven new species of the cavernicolous trechine genus Dongodytes Deuve, 1993 were found and are described: Dongodytes(s. str.)elongatussp. n., Dongodytes(s. str.)troglodytessp. n., Dongodytes(s. str.)lanisp. n., Dongodytes (Dongodytodes) brevipenissp. n., Dongodytes (Dongodytodes) jinzhuensissp. n., Dongodytes (Dongodytodes) inexpectatussp. n. and Dongodytes (Dongodytodes) yaophilussp. n. Diagnoses and notes on the genus, subgenera, and two known species in Du'an Karst, Dongodytes(s. str.)baxian Tian, 2011 and Dongodytes (Dongodytodes) deharvengi Tian, 2011, are also given. A key to subgenera and all species of Dongodytes is provided. To date, Dongodytes becomes one of the richest in species genera of subterranean carabid trechines in China with 12 species which are arranged into two subgenera. Dongodytes (s. str.) Deuve is composed of seven species, four of which from Du'an County, each of other three from Bama, Fengshan and Tian'e Counties, respectively. All species of the subgenus Dongodytodes Tian, 2011 are recorded from Du'an Karst. By having 10 species (nine Dongodytes and one Libotrechus Uéno, 1998), Du'an Karst holds the richest specific diversity of cavernicolous Trechinae in China. Dongodytes species are distributed in a very limited area of the river Hongshui He drainages in northwestern Guangxi, and the river acts as a natural barrier of Dongodytes dispersal at only a specific level. However, all members of Dongodytodes are recorded from the eastern or northern bank of Hongshui He.

A remarkably modified species of the tribe Platynini (Coleoptera, Carabidae) from a limestone cave in Jiangxi Province, eastern China

Morimotoidius zhushandongsp. n. is described and illustrated from a limestone cave called Zhushan Dong II in Wanzhai Xian (=County) of western Jiangxi Province, eastern China. This species is the most modified species within the tribe Platynini in China by having very slender body and appendages, extremely elongated head, and especially, narrowed and barrel-liked pronotum which is as wide as head. However, the above derived characters are autapomorphies to adapt the subterranean environment. M. zhushandongsp. n. must be a troglobite though it has well pigmented body and flat eyes.

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.

A molecular phylogeny of Alpine subterranean Trechini (Coleoptera: Carabidae)

Background

The Alpine region harbours one of the most diverse subterranean faunas in the world, with many species showing extreme morphological modifications. The ground beetles of tribe Trechini (Coleoptera, Carabidae) are among the best studied and widespread groups with abundance of troglobionts, but their origin and evolution is largely unknown.

Results

We sequenced 3.4 Kb of mitochondrial (cox1, rrnL, trnL, nad1) and nuclear (SSU, LSU) genes of 207 specimens of 173 mostly Alpine species, including examples of all subterranean genera but two plus a representation of epigean taxa. We applied Bayesian methods and maximum likelihood to reconstruct the topology and to estimate divergence times using a priori rates obtained for a related ground beetle genus. We found three main clades of late Eocene-early Oligocene origin: (1) the genus Doderotrechus and relatives; (2) the genus Trechus sensu lato, with most anisotopic subterranean genera, including the Pyrenean lineage and taxa from the Dinaric Alps; and (3) the genus Duvalius sensu lato, diversifying during the late Miocene and including all subterranean isotopic taxa. Most of the subterranean genera had an independent origin and were related to epigean taxa of the same geographical area, but there were three large monophyletic clades of exclusively subterranean species: the Pyrenean lineage, a lineage including subterranean taxa from the eastern Alps and the Dinarides, and the genus Anophthalmus from the northeastern Alps. Many lineages have developed similar phenotypes independently, showing extensive morphological convergence or parallelism.

Conclusions

The Alpine Trechini do not form a homogeneous fauna, in contrast with the Pyrenees, and show a complex scenario of multiple colonisations of the subterranean environment at different geological periods and through different processes. Examples go from populations of an epigean widespread species going underground with little morphological modifications to ancient, geographically widespread lineages of exclusively subterranean species likely to have diversified once fully adapted to the subterranean environment.

Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders

Background

The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan–Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group.

Results

Coalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan–Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1–18.6 Ma). Although the Yunnan–Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances.

Conclusions

We concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella highlight the need to conserve these cave spiders.

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km(2) region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete.

Molecular phylogeny of the Trechus brucki group, with description of two new species from the Pyreneo-Cantabrian area (France, Spain) (Coleoptera, Carabidae, Trechinae)

A molecular phylogeny of the species from the Trechus brucki clade (previously Trechus uhagoni group)based on fragments of four mitochondrial genes and one nuclear gene is given. We describe Trechus (Trechus) bouillonisp. n. from the western pre–Pyrenees: Sierras de Urbasa–Andía, Navarra, Spain. The species was collected in mesovoid shallow substratum (mss), a subterranean environment. Molecular as well as morphological evidences demonstrate that the new species belongs to the Trechus brucki clade. A narrow endemic species of high altitude in western French Pyrenees merged with Trechus brucki Fairmaire, 1862a, Trechus bruckoidessp. n., is described. A lectotype is designated for Trechus brucki and Trechus planiusculus Fairmaire, 1862b (junior synonym of Trechus brucki). The species group is redefined based on molecular and morphological characters, and renamed as the brucki group, as Trechus brucki was the first described species of the clade. A unique synapomorphy of the male genitalia, a characteristic secondary sclerotization of the sperm duct, which is shared by all the species of the brucki group sensu novo, is described and illustrated. The Trechus brucki group sensu novo is composed of Trechus beusti (Schaufuss, 1863), Trechus bouillonisp. n., Trechus brucki, Trechus bruckoidessp. n., Trechus grenieri Pandellé, 1867, T. uhagoni uhagoni Crotch, 1869, T. uhagoni ruteri Colas, 1935 and Trechus pieltaini Jeannel, 1920. We discuss the taxonomy of the group and provide illustrations of structures showing the differences between the species, along with distribution data and biogeographical comments.

Beronaphaenops paphlagonicus, a new anophthalmous genus and species of Trechini (Coleoptera, Carabidae) from Turkey

Beronaphaenopsgen. n.paphlagonicussp. n., a new remarkable, eyeless species of Trechini is described from Asian Turkey (type locality: cave Eşek Çukuru Mağarası 2, Milli Park Küre Dağlari, Pinarbasi District, Kastamonu Province). This specialized, troglobite species is characterized by a very peculiar combination of features, including several autapotypic features: mentum tooth large, long and porrect, at distal position reaching or slightly exceeding the level of epilobes, rather slanting ventrally, deeply bifid at the tip; short and fragile paraglossae, hardly surpassing the anterior margin of ligula; absence of posterolateral setae of the pronotum; absence of posterior discal pore in elytral stria 3; apical stylomere shortened, with basal part unusually broadened. The systematic position of the genus amongst the trechine beetles from the peri-Pontic area is discussed. A key to the Anatolian genera of the tribe is prepared.

Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae)

The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini.

Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The relationships of the subtribe Bembidiina were studied in greater detail. Phrypeus is only distantly related to Bembidion, and there is no evidence from sequence data that it belongs within Bembidiina. Three groups that have been recently considered to be outside of the large genus Bembidion are shown to be derived members of Bembidion, related to subgroups: Cillenus is related to the Ocydromus complex of Bembidion, Zecillenus is related to the New Zealand subgenus Zeplataphus, and Hydrium is close to subgenus Metallina. The relationships among major lineages of Trechitae are not, however, resolved with these data.

Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave

Obligatory cave species exhibit dramatic trait modifications such as eye reduction, loss of pigmentation and an increase in touch receptors. As molecular studies of cave adaptation have largely concentrated on vertebrate models, it is not yet possible to probe for genetic universalities underlying cave adaptation. We have therefore begun to study the strongly cave-adapted small carrion beetle Ptomaphagus hirtus. For over 100 years, this flightless signature inhabitant of Mammoth Cave, the world's largest known cave system, has been considered blind despite the presence of residual lens structures. By deep sequencing of the adult head transcriptome, we discovered the transcripts of all core members of the phototransduction protein machinery. Combined with the absence of transcripts of select structural photoreceptor and eye pigmentation genes, these data suggest a reduced but functional visual system in P. hirtus. This conclusion was corroborated by a negative phototactic response of P. hirtus in light/dark choice tests. We further detected the expression of the complete circadian clock gene network in P. hirtus, raising the possibility of a role of light sensation in the regulation of oscillating processes. We speculate that P. hirtus is representative of a large number of animal species with highly reduced but persisting visual capacities in the twilight zone of the subterranean realm. These can now be studied on a broad comparative scale given the efficiency of transcript discovery by next-generation sequencing.

Drosophila as a developmental paradigm of regressive brain evolution: proof of principle in the visual system

Evolutionary developmental biology focuses heavily on the constructive evolution of body plan components, but there are many instances such as parasitism, cave adaptation, or postembryonic growth rate optimization where evolutionary regression is of adaptive value. This is particularly true in the nervous system because of its massive energy costs. However, comparatively little effort has thus far been made to understand the evolutionary developmental trajectories of adaptive nervous system reduction. This review focuses on the organization and evolution of the Drosophila larval brain, which represents an exceptional example of miniaturization, most dramatically in the visual system. It is specifically discussed how the dependency of outer optic lobe development on retinal innervation can be assumed to have facilitated a first evolutionary phase of larval visual system reduction. Afferent input-contingent development of neu- ral compartments very likely plays a widespread role in adaptive brain evolution. Understanding the complete deconstruction of the larval optic neuropiles in Drosophila awaits expanded comparative analysis but has the promise to inform about further developmental trajectories and mechanisms underlying regressive evolution of the brain.

Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

BACKGROUND

The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous.

RESULTS

We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae.

CONCLUSION

Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

Repeated and time-correlated morphological convergence in cave-dwelling harvestmen (Opiliones, Laniatores) from Montane Western North America

BACKGROUND

Many cave-dwelling animal species display similar morphologies (troglomorphism) that have evolved convergent within and among lineages under the similar selective pressures imposed by cave habitats. Here we study such ecomorphological evolution in cave-dwelling Sclerobuninae harvestmen (Opiliones) from the western United States, providing general insights into morphological homoplasy, rates of morphological change, and the temporal context of cave evolution.

METHODOLOGY/PRINCIPAL FINDINGS

We gathered DNA sequence data from three independent gene regions, and combined these data with Bayesian hypothesis testing, morphometrics analysis, study of penis morphology, and relaxed molecular clock analyses. Using multivariate morphometric analysis, we find that phylogenetically unrelated taxa have convergently evolved troglomorphism; alternative phylogenetic hypotheses involving less morphological convergence are not supported by Bayesian hypothesis testing. In one instance, this morphology is found in specimens from a high-elevation stony debris habitat, suggesting that troglomorphism can evolve in non-cave habitats. We discovered a strong positive relationship between troglomorphy index and relative divergence time, making it possible to predict taxon age from morphology. Most of our time estimates for the origin of highly-troglomorphic cave forms predate the Pleistocene.

CONCLUSIONS/SIGNIFICANCE

While several regions in the eastern and central United States are well-known hotspots for cave evolution, few modern phylogenetic studies have addressed the evolution of cave-obligate species in the western United States. Our integrative studies reveal the recurrent evolution of troglomorphism in a perhaps unexpected geographic region, at surprisingly deep time depths, and in sometimes surprising habitats. Because some newly discovered troglomorphic populations represent undescribed species, our findings stress the need for further biological exploration, integrative systematic research, and conservation efforts in western US cave habitats.