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Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies. [ABSTRACT FROM AUTHOR]

Species distribution models (SDMs) have conventionally been used for evaluating the distribution of individual species, but they can also be used, through comparing different SDMs, to evaluate the geographic similarity between taxa. In this study, we used a parasite and host system to infer the geographic overlaps between species with tight biological interaction, for example, parasites and their obligate host. Specifically, we used the horsehair worm Chordodes formosanus and its three mantis hosts to study the extent of niche overlap. We retrieved presence points for the host species and the parasite, and then we built SDMs with MaxEnt implemented in ENMeval using selected bioclim variables (based on variance inflation factor values) at 30s scale. The models showed that the hosts and parasite do not occur in the high elevation areas in Taiwan, which is expected based on their biology. Interestingly, the predicted parasite distribution included areas without collection records, implying local extinction or sampling bias. We subsequently evaluated niche overlap between hosts and the parasite according to five similarity indices (Schoener's D, I statistic, relative rank, Pearson correlation coefficient, and the rank correlation coefficient rho). Our models showed a high similarity of SDM predictions between hosts and the parasite. There were differences among metrics for which host shared the highest similarity with the parasite, but the majority of the results indicated that the Japanese boxing mantis had the highest niche similarity with the horsehair worm. The choice of the niche overlap metric to use can uncover information on the parasite's ecology, which can be important for endangered species. SDMs are reliable tools for host and parasite conservation management and could help improve our understanding of parasite biology and ecology. [ABSTRACT FROM AUTHOR]

Character displacement that leads to divergent phenotypes between sympatric species has been hypothesized to facilitate coexistence and promote the accumulation of biodiversity. However, there are alternative evolutionary mechanisms that may also lead to the evolution of phenotypic divergence between sympatric species; one of the mechanisms is evolutionary contingency. We studied the evolution of the presence and absence of a major male horn phenotype, which may have ecological implications for promoting coexistence between sympatric beetles, across geographic populations from different Xylotrupes beetles. By using a previously published phylogeny with 80 Xylotrupes taxa, we estimated the transition rates between the two phenotypic states (i.e., presence vs. absence of a major male phenotype). Based on the estimated transition rates, we then simulated possible phenotypic outcomes between sympatric species. We found that sympatric species were equally likely to evolve the same versus distinct phenotypic states based on the estimated transition rates given the phylogeny. The empirically observed number of sympatric species showing different phenotypic states can be explained by evolutionary contingency alone. We discussed the importance of applying phylogenetic comparative methods when studying phenotypic evolution and more generally to investigate the effect of stochastic processes before making deterministic inferences. [ABSTRACT FROM AUTHOR]

Consistent and objective species delimitation is crucial to biodiversity studies, but challenges remain when conflicting taxonomic decisions have been made because different data sets and analytical methods were used to delineate species. In the rhinoceros beetle, Xylotrupes siamensis , the use of different morphological characters has resulted in taxonomic disagreement between studies. We used three molecular loci (mitochondrial CO1 and nuclear ITS2 and H3) to investigate the genetic divergence between populations exhibiting different male horn phenotypes. We also applied an approximate Bayesian computation approach to test alternative historical hypotheses that might explain the present genetic diversity among geographical populations. Furthermore, we used species distribution models to estimate the temporal variation in the geographical distribution of suitable habitats. The results show that the two phenotypic taxa within X. siamensis are not genetically structured and that their genetic structure can be explained using isolation by geographical distance. The emergence of the two phenotypic taxa might have been associated with historical isolation in separate refugia. However, spatial expansion and genetic interchange between populations might have gradually eroded the spatial genetic structure. We demonstrate that understanding the historical processes responsible for phenotypic divergence and genetic diversity among current populations could help with making evolutionarily coherent taxonomic decisions. [ABSTRACT FROM AUTHOR]

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species. [ABSTRACT FROM AUTHOR]

Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29 000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short‐winged grasshopper species complex (Melanoplus scudderi group), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that, based on a maximum likelihood molecular phylogeny, each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent‐based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds to the morphologically defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, not only indicating that this trait is labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be primarily associated with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e. fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e. genitalic divergence). [ABSTRACT FROM AUTHOR]

The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern United States and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern United States was investigated. Specifically, genomic data from double-digest restriction-site-associated DNA sequencing libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [ N = 12 individuals] and New Mexico [ N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the 2 geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats. [ABSTRACT FROM AUTHOR]

Aim: The latitudinal diversity gradient is the dominant geographic pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper‐rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (> 1,100 species) ant radiation, Pheidole and test predictions of three general explanations for the latitudinal gradient: variation in diversification rates, tropical conservatism and ecological regulation. Location: Global. Time period: The past 35 million years. Major taxa studied: The hyperdiverse ant genus Pheidole Westwood. Methods: We assembled geographic data for 1,499 species and morphospecies, and inferred a dated phylogeny for 449 species of Pheidole, including 167 species newly sequenced for this study. We tested for correlations between diversification rate and latitude with Bayesian analysis of macroevolutionary mixtures (BAMM), hidden state speciation and extinction (HiSSE), geographic state speciation and extinction (GeoSSE), and a non‐parametric method (FiSSE), evaluated evidence for richness steady state, and examined patterns of diversification as Pheidole spread around the globe. Results: There was no evidence of systematic variation of net diversification rates with latitude across any of the methods. We found that Pheidole diversification occurred in bursts when new continents were colonized, followed by a slowdown in each region, but there is no evidence richness has saturated at an equilibrium in any region. Additionally, we found latitudinal affinity is moderately conserved with a Neotropical ancestor and simulations show that phylogenetic inertia alone is sufficient to produce the gradient pattern. Main conclusions: Our results provide no evidence that diversification rates vary systematically with latitude. Richness is far from steady state in each region, contrary to the ecological regulation hypothesis, although there is evidence that ecological opportunity promotes diversification after colonization of new areas. The fact that niche conservatism is strong enough to produce the gradient pattern is in accord with the tropical conservatism hypothesis. Overall, these results shed light on the mechanisms underlying the emergence of the diversity gradient within the past 34 million years, complementing recent work on deeper time‐scales, and more generally contribute toward much‐needed invertebrate perspective on global biodiversity dynamics. [ABSTRACT FROM AUTHOR]

Taxonomic ranks above the species level are inherently arbitrary. However, there is a growing number of publications aimed at more consistent classifications with comparable ranks among taxa. For this study, we use a recently developed temporal approach that utilizes time-calibrated chronograms to identify and define temporal bands for comparable ordinal and family ranks in Lecanoromycetes, the most diverse lineage of lichen-forming fungi. A multi-locus dataset consisting of 539 taxa in the two major subclasses of Lecanoromycetes, Lecanoromycetidae and Ostropomycetidae, was used to address the circumscription of families and orders. Based on the temporal banding approach, clades that share a common ancestor between 176 and 194 Mya and a time window of 111–135 Mya correspond to order-level and family-level, respectively. Most currently accepted orders and families were supported in their current circumscription, but some new taxa are described. Here we propose a revised, temporally based classification for the two subclasses. Specifically, three new orders are proposed: Sporastatiales, Schaereriales and Thelenellales. Arctomiales, Hymeneliales and Trapeliales are synonymized with Baeomycetales. Varicellariaceae are proposed as a new family, and Diploschistaceae and Thelotremataceae are resurrected. Squamarinaceae and Stereocaulaceae are synonymized with Cladoniaceae, Carbonicolaceae are synonymized with Lecanoraceae, Letrouitiaceae are synonymized with Brigantiaeaceae, Lobariaceae and Nephromataceae are synonymized with Peltigeraceae, Thrombiaceae are synonymized with Protothelenellaceae, and Miltideaceae are synonymized with Agyriaceae. This study represents an important step towards more consistent, comparable deeper-level taxonomic rankings in the most diverse lineages of lichen-forming fungi. [ABSTRACT FROM AUTHOR]

Whether the impact of a specific barrier type is consistent across multiple levels of biodiversity (e.g. populations vs. species) and whether phylogeographical and biogeographical patterns can be structured by the same isolation force have rarely been investigated in evolutionary studies. We investigated the effect of oceanic barriers on genetic divergence among Xylotrupes beetles from the Indo-Australian Archipelago. We found that zoogeographical regions isolated by oceanic trenches were characterized by endemic lineages/species complexes. Dispersal was rare between regions. We further found that populations separated by oceanic barriers were associated with a significantly higher population subdivision compared with populations not separated by oceanic barriers. We did not, however, detect an increased rate of speciation associated with oceanic barriers, implying that the impact of oceanic barriers on population- vs. species-level genetic divergence may have differed. Although our simulation results suggest limited statistical power for detecting concerted divergence, we hypothesize that the concerted action of a barrier at different levels of biodiversity may depend on the mediating effects of the diversification process itself, such as the duration of speciation and the time required for sympatric species to evolve coexistence. [ABSTRACT FROM AUTHOR]

The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic introgression was identified between Hercules beetles living in geographic proximity (parapatric). Phylogenetic relatedness and phenotypic similarity did not predict nor preclude genetic introgression between species. Phenotypic assimilation in body coloration was evident between distantly related Hercules beetles codistributed in Central America, where directional introgression was also statistically supported from the putative donor to receiver lineages. The number of introgressed loci was significantly higher between species with than without phenotypic similarity. I discuss the implications of recent studies on adaptive genetic introgression by providing supporting evidence from the Hercules beetle system. [ABSTRACT FROM AUTHOR]

Biotic interchange between geographic regions can promote rapid diversification. However, what are the important factors that determine the rate of diversification (e.g., trait-dependent diversification) vary between study systems. The evolutionary history of Dynastes beetles, which can be found in both North and South Americas and exhibit two different altitudinal preferences (highland and lowland) is tested for the effects of biotic interchange between continents and different ecological preferences on the rate of species diversification. Additionally, the hypotheses of geological time-dependent and lineage specific diversification rates are also tested. Results from this study indicate that in Dynastes beetles a pre-landbridge dispersal hypothesis from South to North America is preferred and that the speciation rates estimated using BAMM are similar between lineages of different geographic origins and different altitudinal preferences (i.e., diversification rate is not trait-dependent). On the other hand, my result from marcoevolutionary cohort analysis based on BAMM outputs suggests that the rate of speciation in Dynastes beetles is, instead of trait-dependent (geographic and ecological), lineage specific. Furthermore, a steadily increasing speciation rate can be found in Pliocene and Pleistocene, which implies that geological and climatic events, i.e., colonizing North America, habitat reformation in the Amazonia, and forest contraction in Pleistocene, may have together shaped the current biodiversity pattern in Dynastes beetles. [ABSTRACT FROM AUTHOR]

Abstract: Pleistocene glacial oscillations have had profound impacts on the historical population dynamics of extant species. However, the genetic consequences of past climatic changes depend largely on the latitude and topography of the regions in question. This study investigates the effect of Pleistocene glacial periods and the Central Mountain Range on the phylogeography, historical demography, and phenotypic differentiation of a montane forest-dwelling stag beetle, Lucanus formosanus (Coleoptera: Lucanidae), which exhibits extensive mandible variations across mountain ranges in subtropical Taiwan. Analyses of mitochondrial (cox1) and nuclear (wg) loci reveal that L. formosanus originated nearly 1.6 million years ago (Mya) in the early Pleistocene period and consisted of geographically overlapping Alishan and Widespread clades. A drastic population expansion starting approximately 0.2 Mya in the Widespread clade likely resulted from altitudinal range shift of the temperate forests, which was closely tied to the arrival of the Riss glacial period in the late Middle Pleistocene. A ring-like pattern of historical gene flow among neighboring populations in the vicinity of the Central Mountain Range indicates that the mountains constitute a strong vicariant barrier to the east–west gene flow of L. formosanus populations. A geographic cline of decreasing mandible size from central to north and south, and onto southeast of Taiwan is inconsistent with the low overall phylogeographic structures. The degree of mandible variation does not correlate with the expected pattern of neutral evolution, indicating that the evolutionary diversification of this morphological weapon is most likely subject to sexual or natural selection. We hypothesize that the adaptive evolution of mandibles in L. formosanus is shaped largely by the habitat heterogeneity. [ABSTRACT FROM AUTHOR]

Many studies have shown that colour signals are important in spider–insect interactions. The bright body coloration of certain orb-weaving spiders seems to serve as a visual lure to diurnal prey. However, no studies have examined whether this coloration affects spiders'' nocturnal hunting. Some nocturnal lepidopteran pollinators use colour vision to locate their food resources, so orb-weaving spiders'' bright coloration may also be attractive to visually oriented nocturnal insects. To assess the role of body coloration of the orchid spider, Leucauge magnifica, in luring nocturnal prey, we investigated whether: (1) these spiders actively hunt during the night; (2) nocturnal prey comprise a significant proportion of total prey intake; and (3) altering body colour signals significantly affect the nocturnal prey capture rate. Round-the-clock monitoring of L. magnifica activity patterns showed that they hunt more actively at night. Owing to the presence of relatively large moths in their diet at night, L. magnifica consumed higher prey biomass during nocturnal hunting, although this was not statistically significant owing to large variability. Painting over the spiders'' yellow ventrum stripes significantly reduced their moth capture rate. These results show that certain orb-weaving spiders with bright body coloration attract nocturnal prey, and they obtain larger prey from nocturnal hunting. [Copyright &y& Elsevier]

Phylogeographic studies have revealed spatial genetic structure and inferred geographical processes that may have generated genetic diversity and divergence. These study results have implications not only on the processes that generate intraspecific and interspecific diversity but also on the essential integrals for defining evolutionary entities (e.g., species). However, the resulting phylogeographic inferences might be impacted by the sampling design, i.e., the number of individuals per population and the number of geographic populations studied. The effect of sampling bias on phylogeographic inferences remains poorly explored. With a comprehensive sampling design (including 186 samples from 56 localities), we studied the phylogeographic history of a Taiwanese endemic damselfly, Psolodesmus mandarinus, with a specific focus on testing the impact of the sampling design on phylogeographic inference. We found a significant difference in the genetic structure of eastern and western populations separated by the Central Mountain Range (CMR) of Taiwan. However, isolation by the CMR did not lead to reciprocally monophyletic geographic populations. We further showed that, when only a subset of individuals was randomly included in the study, monophyletic geographic populations were obtained. Furthermore, historical demographic expansion could become undetectable when only a subset of samples was used in the analyses. Our results demonstrate the impact of sampling design on phylogeographic inferences. Future studies need to be cautious when inferring the effect of isolation by a physical barrier. [ABSTRACT FROM AUTHOR]

Historical mass extinction events had major impacts on biodiversity patterns. The most recent and intensively studied event is the Cretaceous – Paleogene (K-Pg) boundary (ca. 66 million years ago [MYA]). However, the factors that may have impacted diversification dynamics vary across lineages. We investigated the macroevolutionary dynamics with a specific focus on the impact of major historical events such as the K-Pg mass extinction event on two major subclasses – Lecanoromycetidae and Ostropomycetidae – of lichen-forming fungi and tested whether variation in the rate of diversification can be associated with the evolution of a specific trait state - macrolichen. Our results reveal accelerated diversification events in three families of morphologically complex lichen-forming fungi – Cladoniaceae, Parmeliaceae, and Peltigeraceae – which are from the subclass Lecanoromycetidae and mostly composed of macrolichens, those that form three dimensional structures. Our RTT plot result for the subclass Lecanoromycetidae also reveals accelerated diversification. Changes in diversification rates occurred around the transition between Mesozoic and Cenozoic eras and was likely related to the K-Pg mass extinction event. The phylogenetic positions for rate increases estimated based on marginal shift probability are, however, scattered from 100 to 40 MYA preventing us from making explicit inference. Although we reveal that the phenotypic state of macrolichens is associated with a higher diversification rate than microlichens, we also show that the evolution of macrolichens predated the K-Pg event. Furthermore, the association between macrolichens and increased diversification is not universal and can be explained, in part, by phylogenetic relatedness. By investigating the macroevolutionary dynamics of lichen-forming fungi our study provides a new empirical system suitable to test the effect of major historical event on shaping biodiversity patterns and to investigate why changes in biodiversity patterns are not in concordance across clades. Our results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. However, future studies focusing on individual lichen-forming fungal families are required to ascertain whether diversification rates are associated with growth form and certain geological events. [ABSTRACT FROM AUTHOR]

Aim: The Southern Ocean landmasses have intrigued biologists for centuries because they share many taxonomic groups. Such disjunct taxa can provide insight into evolutionary processes that connect populations or drive divergence. The lichenized fungus Pseudocyphellaria glabra, for example, has a disjunct distribution—separated by the Tasman Sea and the Pacific Ocean—yet whether these locations should be genetically distinct is unclear. The large distances between continents may be expected to prohibit gene flow, but strong and sustained winds in the Southern Hemisphere and the small size of P. glabra propagules may facilitate migration. We compared support for these two hypotheses. Location: Southeastern Australia, Tasmania, New Zealand and Southern Chile. Taxon: Pseudocyphellaria glabra (Hook. f. & Taylor) C.W. Dodge, 1948 (Ascomycota, Peltigeraceae) Methods: We collected 371 samples across the disjunct range of P. glabra. We generated genomic data using restriction site‐associated DNA sequencing and reconstructed a Maximum Likelihood phylogeny using 29,098 unlinked SNPs. We then conducted population genomic analyses using 3,756 SNPs including a minimum‐spanning network, principal components analysis, discriminate analysis of principal components, and k‐means clustering. Results: Maximum likelihood analysis recovered multiple well‐supported clades that roughly corresponded to geography. Population genomic analyses identified genetic structuring that generally corresponded with geographic distance; however, some individuals from Chile and Australia were assigned to genetic clusters found in New Zealand, suggesting that recent dispersal events from New Zealand have successfully colonized Chile and Australia. Main conclusion: Populations of P. glabra from Australia, Chile and New Zealand are genetically distinct, but frequent long‐distance dispersal during the Quaternary probably prevented speciation. This study demonstrates the power of restriction‐site associated DNA sequencing for discernment between divergent and connective evolutionary forces that simultaneously influence the population structure of species with disjunct ranges in the Southern Ocean landmasses. [ABSTRACT FROM AUTHOR]

Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high‐quality chromosome‐level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo‐chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi‐C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate‐gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Multiple evidences were incorporated into species delimitation of the Primulina hochiensis complex. • Genetic data and the multispecies coalescent methods (MSC) revealed five genetic lineages as species. • Principal component analysis (PCA) of morphological data recovered three distinct clusters. • The coalescent species delimitation methods may over-estimate species diversity with strong genetic structure. • A new species, P. lianpingensis , was described. Abstract To consistently and objectively delineate species-level divergence from population subdivision has been a challenge in systematics. This is particularly evident in naturally fragmented and allopatric systems in which small population size often leads to extreme population structuring. Here we evaluated the robustness of the species delimitation methods implemented in BEAST, BPP, and iBPP in the Primulina hochiensis complex comprising four described and one candidate species (five taxa in total) distributed in karst landscapes of southern China. We analyzed levels of molecular and morphological divergence among species using multilocus sequence data (nine chloroplast loci and 10 nuclear loci), and morphological data (16 quantitative and 12 qualitative traits), for 124 individuals from 25 populations of the complex. Independent analyses of cpDNA and nDNA sequence data revealed high levels of genetic differentiation among the five taxa. Both BPP and iBPP delimited five candidate species, which correspond to the five genetic clusters recovered with population structure analysis. In contrast, morphological differences among populations were more limited, so that results from principal component analysis (PCA) recovered only three distinct clusters. We ruled out the possibility of morphologically cryptic species because reciprocally monophyletic groups were not supported among the morphologically un-differentiated taxa. Our results represent a case where extreme population genetic structuring leads to oversplit of species diversity by molecular data using the multispecies coalescent (MSC) methods. The observed congruence across multiple analyses corroborates the recognition of a new species P. lianpingensis and indicates its sister species relationship with P. yingdeensis. This study highlights the dangers of violating model assumption and the importance of incorporating multiple evidence into species delimitation of a particular system. [ABSTRACT FROM AUTHOR]

Forest soil and leaf litter support diverse arthropod mesofauna for which diversity dynamics is challenging to study due to the high number of species and specimens, small body size and limited taxonomic knowledge.Immature stages (larvae) are even harder to identify than adults, as their morphology is largely unknown. Therefore, larvae are often ignored, even though they may form a substantial proportion of specimens collected, are less mobile than adults and their exclusion may provide an incomplete diversity profile.Here, we use Oxford Nanopore DNA barcoding to investigate whether the inclusion of larvae provides a more complete taxonomic, phylogenetic and functional diversity profiles in leaf litter beetles (Coleoptera) from a subtropical forest in Taiwan.Our results indicate that larvae represent up to 38% of beetle specimens per sample, but most of them belong to 2–3 common species. Larvae of most beetle species are rarely collected repeatedly or in multiple specimens, possibly due to special habitat requirements or high seasonality.Taxonomic, phylogenetic and incidence‐based functional diversity measures were not affected by the exclusion of larvae in the Staphylinidae dataset but were strongly biased in all‐beetle dataset, especially when only common or abundant species were considered. Taxonomic beta diversity was not affected by the omission of larvae.Our results indicate that immature stages may be omitted in ecological studies of arthropods in case both adults and larvae co‐occur in the same habitat, and the sites are sampled repeatedly. Caution is needed (1) in groups in which larvae and adults do not inhabit the same environment or strongly differ in biology, (2) when rare species are omitted or (3) when functional diversity is calculated from abundance data. [ABSTRACT FROM AUTHOR]

1.We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedent rate of decline.2.However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remains challenging.3.We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex.4.We found that the three sky‐island taxa formed three independently evolving units without detectable post‐divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid‐Pleistocene, have experienced episodes of demographic decline in the past.5.More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesised to impact the recent demographic history (<100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa.6.We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1. [ABSTRACT FROM AUTHOR]

Alpha taxonomy is fundamental for many biological fields. Delineation of the species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets, and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialisation, and further corroborate that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can occur at a small geographic scale, even in a winged insect like tiger beetles. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered. ZooBank LSID: urn:lsid:zoobank.org:pub:9DEC1432-365C-4872-8D06-73B95F30624F Estimating species diversity is critical for all biological fields but objectively determining species diversity can be challenging. We investigated the speciation history and explored the species diversity in a tiger beetle species complex using an integrative approach. We also demonstrated that allopatric speciation and population subdivision could occur at fine geographic scale even if the system has been expected to exhibit high dispersal ability. Therefore, neglected species diversity may still hide in plain sight in many empirical systems. [ABSTRACT FROM AUTHOR]

Abstract: This study determined the first complete mitochondrial genome of a damselfly, Euphaea formosa (Insecta: Odonata: Zygoptera), and reconstructed a phylogeny based on thirteen protein-coding genes of mitochondrial genomes in twenty-five representative hexapods to examine the relationships among the basal Pterygota. The damselfly''s mitochondrial genome is a circular molecule of 15,700bp long, and contains the entire set of thirty-seven genes typically found in insects. The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar across the three odonate species, suggesting a conserved genome evolution within the Odonata. The presence of the intergenic spacer s5 likely represents a synapomorphy for the dragonflies (Anisoptera). Maximum parsimony, maximum likelihood, and Bayesian analyses of both nucleotide and amino acid sequences cannot support the three existing phylogenetic hypotheses of the basal Pterygota (Palaeoptera, Metapterygota, and Chiastomyaria). In contrast, the phylogenetic results indicate an alternative hypothesis of a strongly supported basal Odonata and a sister relationship of the Ephemeroptera and Plecoptera. The unexpected sister Ephemeroptera+Plecoptera clade, which contradicts with the widely accepted hypothesis of a monophyletic Neoptera, requires further analyses with additional mitochondrial genome sampling at the base of the Neoptera. [Copyright &y& Elsevier]

Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis , from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions. [ABSTRACT FROM AUTHOR]

[Display omitted] • The most comprehensive Stathmopodidae phylogeny to date, focusing on fern-spore-feeding Cuprininae. • Systematic revision of Cuprininae enhances understanding of insect-fern interactions, diverging from angiosperm-centric studies. • Despite fern spores being rare niche for Lepidoptera, no significant differences in Speciation/Extinction/State-transition rates between fern-spore feeders and others. • State-transition rate differs between specialists and oligophages; faster transition from oligophages to specialists observed. Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonoda gen. nov. , Petala gen. nov. , and Pediformis gen. nov. , and revalidating five genera: Cuprina , Calicotis , Thylacosceles , Actinoscelis , Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae. [ABSTRACT FROM AUTHOR]

A basic expectation of evolution by natural selection is that species morphologies will adapt to their ecological niche. In social organisms, this may include selective pressure from the social environment. Many non-ant parasites of ant colonies are known to mimic the morphology of their host species, often in striking fashion 1 , 2 , indicating there is selection on parasite morphology to match the host (Batesian and/or Wasmannian mimicry 3). However, ants that parasitize other ant societies are usually closely related to their hosts (Emery's rule) 4–8 and expected to be similar due to common ancestry, making any kind of mimicry difficult to detect 9. Here, we investigate the diversification of the hyperdiverse ant genus Pheidole in Madagascar, including the evolution of 13 putative social parasite species within a broader radiation of over 100 ant species on the island. We find that the parasitic species are monophyletic and that their associated hosts are spread across the Malagasy Pheidole radiation. This provides an opportunity to test for selection on morphological similarity and divergence between parasites and hosts. Using X-ray microtomography and both linear measurements and three-dimensional (3D) geometric morphometrics, we show that ant social parasite worker morphologies feature a mix of "host-matching" and "parasitic" traits, where the former converge on the host phenotype and the latter diverge from typical Pheidole phenotypes to match a common parasitic syndrome. This finding highlights the role of social context in shaping the evolution of phenotypes and raises questions about the role of morphological sensing in nestmate recognition. • A monophyletic group of Malagasy Pheidole ants parasitizes congeneric host species • Host species are not the closest relatives of parasites; Emery's rule does not apply • 2D and 3D analyses show parasite morphology tends to match their host • Morphological sensing by hosts is proposed as a selective force (Wasmannian mimicry) Fischer, Friedman et al. find an interesting clade of ants that parasitize other, closely related ants from Madagascar. Morphological analyses reveal that parasite morphology evolves to match host morphology, raising questions about the role of morphological sensing in social insect recognition systems. [ABSTRACT FROM AUTHOR]

Phenotypic traits are often integrated into evolutionary modules: sets of organismal parts that evolve together. In social insect colonies, the concepts of integration and modularity apply to sets of traits both within and among functionally and phenotypically differentiated castes. On macroevolutionary timescales, patterns of integration and modularity within and across castes can be clues to the selective and ecological factors shaping their evolution and diversification. We develop a set of hypotheses describing contrasting patterns of worker integration and apply this framework in a broad (246 species) comparative analysis of major and minor worker evolution in the hyperdiverse ant genus Pheidole. Using geometric morphometrics in a phylogenetic framework, we inferred fast and tightly integrated evolution of mesosoma shape between major and minor workers, but slower and more independent evolution of head shape between the two worker castes. Thus, Pheidole workers are evolving as a mixture of intracaste and intercaste integration and rate heterogeneity. The decoupling of homologous traits across worker castes may represent an important process facilitating the rise of social complexity. [ABSTRACT FROM AUTHOR]

A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta , by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species. [ABSTRACT FROM AUTHOR]

Species richness is not evenly distributed across the tree of life and a limited number of lineages comprise an extraordinarily large number of species. In lichen-forming fungi, only two genera are known to be ‘ultradiverse’ (>500 species), with the most diverse genus, Xanthoparmelia, consisting of c. 820 species. While Australia and South Africa are known as current centres of diversity for Xanthoparmelia, it is not well known when and where this massive diversity arose. To better understand the geographical and temporal context of diversification in this diverse genus, we sampled 191 Xanthoparmelia specimens representing c. 124 species/species-level lineages from populations worldwide. From these specimens, we generated a multi-locus sequence data set using Sanger and high-throughput sequencing to reconstruct evolutionary relationships in Xanthoparmelia, estimate divergence times and reconstruct biogeographical histories in a maximum likelihood and Bayesian framework. This study corroborated the phylogenetic placement of several morphologically or chemically diverse taxa within Xanthoparmelia, such as Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Omphalodiella, Paraparmelia, Placoparmelia and Xanthomaculina, in addition to improved phylogenetic resolution and reconstruction of previously unsampled lineages within Xanthoparmelia. Our data indicate that Xanthoparmelia most likely originated in Africa during the early Miocene, coinciding with global aridification and development of open habitats. Reconstructed biogeographical histories of Xanthoparmelia reveal diversification restricted to continents with infrequent intercontinental exchange by long-distance dispersal. While likely mechanisms by which Xanthoparmelia obtained strikingly high levels of species richness in Australia and South Africa remain uncertain, this study provides a framework for ongoing research into diverse lineages of lichen-forming fungi. Finally, our study highlights a novel approach for generating locus-specific molecular sequence data sets from high throughput metagenomic reads. [ABSTRACT FROM AUTHOR]

• Comprehensive molecular phylogeny of the Holarctic clade of lichen-forming fungi genus Xanthoparmelia. • Despite reconstructing relatively consistent phylogenetic trees, rampant phylogenetic conflict was revealed. • Widespread hybridization was detected among species in the most diverse genus of lichen-forming fungi using three independent tests for hybridization. While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. As Xanthoparmelia is projected to have gone through recent, rapid diversification, this genus is particularly suitable for investigating and interpreting the origins of phylogenomic conflict. Focusing on a clade of Xanthoparmelia largely restricted to the Holarctic region, we used a genome skimming approach to generate 962 single-copy gene regions representing over 2 Mbp of the mycobiont genome. From this genome-scale dataset, we inferred evolutionary relationships using both concatenation and coalescent-based species tree approaches. We also used three independent tests for hybridization. Although different species tree reconstruction methods recovered largely consistent and well-supported trees, there was widespread incongruence among individual gene trees. Despite challenges in differentiating hybridization from ILS in situations of recent rapid radiations, our genome-wide analyses detected multiple potential hybridization events in the Holarctic clade, suggesting one possible source of trait variability in this hyperdiverse genus. This study highlights the value in using a pluralistic approach for characterizing genome-scale conflict, even in groups with well-resolved phylogenies, while highlighting current challenges in detecting the specific impacts of hybridization. [ABSTRACT FROM AUTHOR]