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The invasive eucalyptus tortoise beetle, Paropsis charybdis, defoliates plantations of Eucalyptus nitens in New Zealand. Recent efforts to identify host specific biological control agents (parasitoids) from Tasmania, Australia, have focused on the larval parasitoid wasp, Eadya paropsidis (Braconidae), first described in 1978. In Tasmania, Eadya has been reared from Paropsisterna agricola (genus abbreviated Pst.), a smaller paropsine that feeds as a larva on juvenile rather than adult foliage of Eucalyptus nitens. To determine which of the many paropsine beetle hosts native to Tasmania are utilized by E. paropsidis, and to rule out the presence of cryptic species, a molecular phylogenetic approach was combined with host data from rearing experiments from multiple locations across six years. Sampling included 188 wasps and 94 beetles for molecular data alone. Two mitochondrial genes (COI and Cytb) and one nuclear gene (28S) were analyzed to assess the species limits in the parasitoid wasps. The mitochondrial genes were congruent in delimiting four separate phylogenetic species, all supported by morphological examinations of Eadya specimens collected throughout Tasmania. Eadya paropsidis was true to the type description, and was almost exclusively associated with P. tasmanica. A new cryptic species similar to E. paropsidis, Eadya sp. 3, was readily reared from Pst. agricola and P. charybdis from all sites and all years. Eadya sp. 3 represents the best candidate for biological control of P. charybdis and was determined as the species undergoing host range testing in New Zealand for its potential as a biological control agent. Another new species, Eadya sp. 1, was morphologically distinctive and attacked multiple hosts. The most common host was Pst. variicollis, but was also reared from Pst. nobilitata and Pst. selmani. Eadya sp. 1 may have potential for control against Pst. variicollis, a new incursion in New Zealand, and possibly Pst. selmani in Ireland. Our molecular data suggests that Pst. variicollis is in need of taxonomic revision and the geographic source of the beetle in New Zealand may not be Tasmania. Eadya sp. 2 was rarely collected and attacked P. aegrota elliotti and P. charybdis. Most species of Eadya present in Tasmania are not host specific to one beetle species alone, but demonstrate some host plasticity across the genera Paropsisterna and Paropsis. This study is an excellent example of collaborative phylogenetic and biological control research prior to the release of prospective biological control agents, and has important implications for the Eucalyptus industry worldwide. [ABSTRACT FROM AUTHOR]

The critically endangered spotted handfish (Brachionichthys hirsutus) is restricted to a limited number of locations in south-eastern Tasmania, Australia. As is often the case for rare species, conducting statistically adequate surveys for B. hirsutus can be costly and time consuming due to the low probability of encountering individuals. For the first time we used a highly efficient and rigorous Global Positioning System (GPS) parameterised underwater visual census (GUVC) to survey B. hirsutus abundance within all nine known local populations in the Derwent Estuary within one season. In addition, a benthic microhabitat assessment was conducted simultaneously using a GoPro® camera attached to diver to determine B. hirsutus microhabitat preferences. B. hirsutus local populations varied between sites, with densities ranging from 1.58 to 43.0 fishes per hectare. B. hirsutus demonstrates a strong preference for complex microhabitat features, such as depressions and ripple formations filled with biogenic substrates (e.g. shells) but avoids simple, low relief microhabitats (e.g. sand flats) and areas dominated by ephemeral, filamentous algae. Complex microhabitats may enable B. hirsutus to avoid predators, increase forage opportunities or provide higher quality spawning sites. This first wide-scale application of GUVC for B. hirsutus allowed us to survey a larger number of sites than previously possible to provide a robust reference point for future long-term monitoring. [ABSTRACT FROM AUTHOR]

Surveying terrestrial species across diverse habitats is important for predicting species’ distributions and implementing conservation actions. For vocalising species, passive acoustic monitoring (PAM) is increasing in popularity; however, survey design rarely considers the factors influencing the timing and occurrence of vocalisations and in turn, how they may influence detectability of the species. Here, we use the koala (Phascolarctos cinereus) as a case study to show how PAM can be used to first examine the factors influencing vocalisations, and then use occupancy modelling to make recommendations on survey design for the species. We used automated recording units to monitor koala vocalisations at ten sites between August 2016 and January 2017. The timing of male koala vocalisations was linked to time of sunset with vocalisations increasing two hours prior to sunset and peaking at four hours after sunset. Vocalisations had a seasonal trend, increasing from the early to middle stage of the breeding season. Koala population density and stage of the breeding season had more influence on detection probability than daily sampling schedule. Where population density was low, and during the early stage of the breeding season, 7 survey nights (recording for 6 hours from 20:00h to 02:00h; i.e. the period of peak bellowing activity) were required to be 95% confident of a site-specific absence. Our study provides an approach for designing effective passive acoustic surveys for terrestrial species. [ABSTRACT FROM AUTHOR]

The southern region of Brazil is characterized by high species diversity and endemism of freshwater fishes distributed across geographically isolated river basins. Microglanis cottoides has a widespread range across these river basins and occurs in sympatry with other endemic species of the genus (e.g. M. cibelae, M. eurystoma, and M. malabarbai). Herein we tested the monophyly of M. cottoides and presented for the first time information about the molecular phylogeny of species in the genus. The results suggest that M. cottoides currently forms a non-monophyletic group which includes populations endemic to the Uruguay River basin that are more closely related to M. malabarbai, and excludes M. cibelae, found to be nested within M. cottoides. Based on an integrative approach using morphological and molecular data, we propose M. cibelae as a junior synonym of M. cottoides, and the populations of the Uruguay River basin previously assigned to M. cottoides in fact belong to M. malabarbai. Our molecular phylogeny shows that M. cottoides is sister to M. parahybae, which is also a coastal species, and M. malabarbai is sister of M. garavelloi, both endemic to inland river basins. The time-calibrated phylogeny indicates that the separation between inland and the coastal clades occurred in the Tertiary period, and that the species within the coastal basins diverged in the Pliocene, which overlaps with the diversification times estimated for the two inland species as well. This pattern of diversification corroborates some previous studies with other fishes from the same region. [ABSTRACT FROM AUTHOR]

The biogeographical history of Afro-tropical lowland forests during the Plio-Pleistocene is characterized by pervasive fragmentation-coalescence cycling due to global climatic oscillations. Vicariance scenarios driven by forest fragmentation have long been hypothesized as major mechanisms for the creation and maintenance of Afro-tropical avian diversity. However, the timing and centre of diversification events remains unclear. We undertook the first molecular phylogenetic and biogeographic investigation of the avian genus Criniger, a group of understory birds endemic to the lowland forests of West and Central Africa. Utilizing DNA from 43 specimens and a combination of molecular and biogeographic methods, we constructed time-calibrated phylogenies and ancestral area estimations. We estimated a widespread origin for the genus, with a basal divergence dating to the late Miocene. All other speciation events were dated to the Pliocene. However, we recovered substantial geographic structuring of genetic diversity, dating to the Pleistocene, within both Western and Central Africa for three species. The biogeographic patterns observed in the genus Criniger are likely the result of allopatric diversification driven by forest fragmentation during the Plio-Pleistocene. The results of this study indicate that Afro-tropical forests harbour substantially higher levels of cryptic diversity and greater genetic complexity than previously hypothesized. [ABSTRACT FROM AUTHOR]

We investigate mitochondrial (COI, 16S rDNA) and nuclear (ITS2, 28S rDNA) genetic structure of North East Atlantic lineages of Terebellides, a genus of sedentary annelids mainly inhabiting continental shelf and slope sediments. We demonstrate the presence of more than 25 species of which only seven are formally described. Species boundaries are determined with molecular data using a broad range of analytical methods. Many of the new species are common and wide spread, and the majority of the species are found in sympatry with several other species in the complex. Being one of the most regularly encountered annelid taxa in the North East Atlantic, it is more likely to find an undescribed species of Terebellides than a described one. [ABSTRACT FROM AUTHOR]

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species. [ABSTRACT FROM AUTHOR]

The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H. obsoletus. Host-plant use was confirmed for Convolvulus arvensis, Urtica dioica, Vitex agnus-castus and Crepis foetida. Mitochondrial genetic analysis showed sympatric occurrence of three phylogenetic lineages that were ecologically delineated by host-plant preference, but were morphologically inseparable. Nuclear data supported the existence of three genetic groups (Evanno’s ΔK(3) = 803.72) with average genetic membership probabilities > 90%. While populations associated with C. arvensis and U. dioica form a homogenous group, populations affiliated with V. agnus-castus and C. foetida constitute two independent plant-associated lineages. The geographical signal permeating the surveyed populations indicated complex diversification processes associated with host-plant selection and likely derived from post-glacial refugia in the eastern Mediterranean. This study provides evidence for cryptic species diversification within H. obsoletus sensu lato: i) consistent mitochondrial differentiation (1.1–1.5%) among host-associated populations in syntopy and in geographically distant areas, ii) nuclear genetic variance supporting mitochondrial data, and iii) average mitochondrial genetic distances among host-associated meta-populations are comparable to the most closely related, morphologically distinguishable species, i.e., Hyalesthes thracicus (2.1–3.3%). [ABSTRACT FROM AUTHOR]

Invasive snails in the genus Pomacea have spread across Southeast Asia including Peninsular Malaysia. Their effects on natural and agricultural wetlands are appreciable, but species-specific effects are less clear because of morphological similarity among the species. Our objective was to establish diagnostic characteristics of Pomacea species in Malaysia using genetic and morphological criteria. The mitochondrial COI gene of 52 adult snails from eight localities in Peninsular Malaysia was amplified, sequenced, and analysed to verify species and phylogenetic relationships. Shells were compared using geometric morphometric and covariance analyses. Two monophyletic taxa, P. canaliculata and P. maculata, occurred in our samples. The mean ratio of shell height: aperture height (P = 0.042) and shell height: shell width (P = 0.007) was smaller in P. maculata. P. maculata co-occurred with P. canaliculata in five localities, but samples from three localities contained only P. canaliculata. This study is the first to confirm the presence of two of the most invasive species of Pomacea in Peninsular Malaysia using a molecular technique. P. canaliculata appears to be the more widespread species. Despite statistical differences, both quantitative and qualitative morphological characteristics demonstrated much interspecific overlap and intraspecific variability; thus, shell morphology alone cannot reliably verify species identity. Molecular techniques for distinguishing between these two highly invasive Pomacea species are needed to understand their specific ecological niches and to develop effective protocols for their management. [ABSTRACT FROM AUTHOR]

Ototyphlonemertes is a cosmopolitan genus of meiofaunal nemerteans. Their morphological characters are insufficient to reliably identify and delimit species. Consequently, some of the species are considered cosmopolitan despite anticipated low dispersion capability of the adults and a short planktonic larval phase. Indeed, recent studies show that some species actually comprise cryptic species, and populations are connected by stochastic events of long-distance dispersion. Based solely on morphological traits, a Lactea and a Pallida morph of Ototyphlonemertes are recognized here from collections at eight and five locations respectively along the Chilean coast. To assess the phylogeographic patterns of their populations, two mitochondrial markers (COI and COX3) of 162 specimens of Lactea and 25 of Pallida were sequenced. Final sequences are 605bp and 362bp for COI and COX3, respectively. Results from phylogenetic and haplotype network analyses suggest that the Lactea morph comprises up to three independent evolutionary units (one with only COX3 sequences). A COI gene tree including other previously published Ototyphlonemertes sequences groups the Chilean Lactea with other Lactea, while the Chilean Pallida is grouped with other Pallida. Different structuring and gene flow patterns found for the four groups support the hypothesis that these are four independent evolutionary entities with different ecological, dispersal and demographical characteristics. [ABSTRACT FROM AUTHOR]

Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior. [ABSTRACT FROM AUTHOR]

Anti-predator signaling is highly variable with numerous examples of species employing cryptic coloration to avoid detection or conspicuous coloration (often coupled with a secondary defense) to ensure detection and recollection. While the ends of this spectrum are clear in their function, how species use intermediate signals is less clear. Australian Brood Frogs (Pseudophryne) display conspicuous coloration on both their dorsum and venter. Coupled with the alkaloid toxins these frogs possess, this coloration may be aposematic, providing a protective warning signal to predators. We assessed predation rates of known and novel color patterns and found no difference for avian or mammalian predators. However, when Pseudophryne dorsal phenotypes were collectively compared to the high-contrast ventral phenotype of this genus, we found birds, but not mammals, attacked dorsal phenotypes significantly less frequently than the ventral phenotype. This study, importantly, shows a differential predator response to ventral coloration in this genus which has implications for the evolution of conspicuous signaling in Pseudophryne. [ABSTRACT FROM AUTHOR]

ABSTRACT Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus. IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species. [ABSTRACT FROM AUTHOR]

Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S. mortenseni) with the goal of clarifying its taxonomic content and geographic range boundaries for conservation. We present evidence that the current concept of S. nigrovittata contains at least eight species, two of which are each known from only two localities, but that S. mortenseni is more geographically widespread than currently realized. Five of these species are described as new to science. [ABSTRACT FROM AUTHOR]

Southwestern Australia is one of the global biodiversity hotspots. Like many other hotspots, comparatively few data are available explaining speciation patterns in endemic animal lineages, which hampers conservation efforts and a deeper understanding of how diversity is generated and maintained. I investigated the phylogeographic structure of an ancient arachnid species, the pseudoscorpion Pseudotyrannochthonius giganteus Beier, 1971, endemic to the mesic eucalypt forests of southwestern Australia. This species is habitat-restricted and has morphologically divergent populations in epigean (forest) and hypogean (karst) habitats. Phylogenetic, molecular clock and population genetic analyses of mitochondrial (COI mtDNA) and nuclear (ITS2 rDNA) data revealed a complex population structure, with six allopatric lineages separated by vicariant barriers, such as rivers. These lineages diverged between the late Miocene and Pliocene epochs, characterised by increasingly intense climatic cycles between mesic/warm and arid/cold. Surprisingly, specimens from caves were genetically similar to those from forests, indicating subterranean isolation has not driven diversification. Instead, genetic diversity is clustered in a small area, coinciding with the highest rainfall and lowest seasonality in Western Australia. Future climates, warmer and drier than today, will likely lead to range retraction towards this area and mimic past variations that have shaped contemporary diversity. Southwestern Australia is an ancient, stable landscape that allowed for persistence of ancient lineages, such as P. giganteus . Historic climatic fluctuations have driven diversification, generating highly structured species and localised centres of endemism. Other ancient landscapes, e.g. South Africa’s Cape Provinces, are expected to share similarly complex patterns of invertebrate biodiversity. Unravelling these is essential to informed conservation decision making. [ABSTRACT FROM AUTHOR]

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region. [ABSTRACT FROM AUTHOR]

African forest elephants face severe threats from illegal killing for ivory and bushmeat and habitat conversion. Due to their cryptic nature and inaccessible range, little information on the biology of this species has been collected despite its iconic status. Compiling individual based monitoring data collected over 20 years from the Dzanga Bai population in Central African Republic, we summarize sex and age specific survivorship and female age specific fecundity for a cohort of 1625 individually identified elephants. Annual mortality (average = 3.5%) and natality (average = 5.3%) were lower and markedly less variable relative to rates reported for savanna elephant populations. New individuals consistently entered the study system, leading to a 2.5% average annual increase in the registered population. Calf sex ratios among known birth did not differ from parity. A weak seasonal signal in births was detected suggesting increased conceptions during the wet season. Inter-calf intervals and age of primiparity were longer relative to savanna elephant populations. Within the population, females between the ages of 25–39 demonstrated the shortest inter-calf intervals and highest fecundity, and previous calf sex had no influence on the interval. Calf survivorship was high (97%) the first two years after birth and did not differ by sex. Male and female survival began to differ by the age of 13 years, and males demonstrated significantly lower survival relative to females by the age of 20. It is suspected these differences are driven by human selection for ivory. Forest elephants were found to have one of the longest generation times recorded for any species at 31 years. These data provide fundamental understanding of forest elephant demography, providing baseline data for projecting population status and trends. [ABSTRACT FROM AUTHOR]

Advertisement calls are often used as essential basic information in studies of animal behaviour, ecology, evolution, conservation, taxonomy or biodiversity inventories. Yet the description of this type of acoustic signals is far to be completed, especially in tropical regions, and is frequently non-standardized or limited in information, restricting the application of bioacoustics in science. Here we conducted a scientometric review of the described adverstisement calls of anuran species of Brazil, the world richest territory in anurans, to evaluate the amount, standard and trends of the knowledge on this key life-history trait and to identify gaps and directions for future research strategies. Based on our review, 607 studies have been published between 1960 to 2016 describing the calls of 719 Brazilian anuran species (68.8% of all species), a publication rate of 10.6 descriptions per year. From each of these studies, thirty-one variables were recorded and examined with descriptive and inferential statistics. In spite of an exponential rise over the last six decades in the number of studies, described calls, and quantity of published metadata, as revealed by regression models, clear shortfalls were identified with regard to anuran families, biomes, and categories of threat. More than 55% of these species belong to the two richest families, Hylidae or Leptodactylidae. The lowest percentage of species with described calls corresponds to the most diverse biomes, namely Atlantic Forest (65.1%) and Amazon (71.5%), and to the IUCN categories of threat (56.8%), relative to the less-than-threatened categories (74.3%). Moreover, only 52.3% of the species have some of its calls deposited in the main scientific sound collections. Our findings evidence remarkable knowledge gaps on advertisement calls of Brazilian anuran species, emphasizing the need of further efforts in standardizing and increasing the description of anuran calls for their application in studies of the behaviour, ecology, biogeography or taxonomy of the species. [ABSTRACT FROM AUTHOR]

Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP). However, several important evolutionary questions, such as the distribution of chromosome numbers and whether the diploid condition is dominant over a potential polyploid condition driving the evolution and diversity in floral morphology and breeding systems in this cactus, are still unclear. In this study, we determined chromosome numbers in 11 localities encompassing virtually the entire geographic range of distribution of P. pringlei. Our data revealed the first diploid (2n = 22) count in this species restricted to the hermaphroditic populations of Catalana (ICA) and Cerralvo (ICE) Islands, whereas the tetraploid (2n = 44) condition is consistently distributed throughout the BCP and mainland Sonora populations distinguished by a non-hermaphroditic breeding system. These results validate a wider distribution of polyploid relative to diploid individuals and a shift in breeding systems coupled with polyploidisation. Considering that the diploid base number and hermaphroditism are the proposed ancestral conditions in Cactaceae, we suggest that ICE and ICA populations represent the relicts of a southern diploid ancestor from which both polyploidy and unisexuality evolved in mainland BCP, facilitating the northward expansion of this species. This cytogeographic distribution in conjunction with differences in floral attributes suggests the distinction of the diploid populations as a new taxonomic entity. We suggest that chromosome doubling in conjunction with allopatric distribution, differences in neutral genetic variation, floral traits, and breeding systems has driven the reproductive isolation, evolution, and diversification of this columnar cactus. [ABSTRACT FROM AUTHOR]

The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A . janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A . janus , likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation. [ABSTRACT FROM AUTHOR]

High morphological homogeneity and cryptic speciation may cause the diversity within Simuliidae to be underestimated. Recent molecular studies on population genetics and phylogeography have contributed to reveal which factors influenced the diversity within this group. This study aimed at examining the genetic diversity of Simulium hirtipupa Lutz, 1910 in populations from the biomes Caatinga, Cerrado, and Atlantic Forest. In this study, we carried out phylogeographic and population genetic analyses using a fragment of the mitochondrial gene COI. The 19 populations studied were clustered into seven groups, most of which are associated with geography indicating certain genetic structure. The northern region of the state of Minas Gerais is most likely the center of origin of this species. The average intergroup genetic distance was 3.7%, indicating the presence of cryptic species. The species tree as well as the haplotype network recovered all groups forming two major groups: the first comprises groups Gr-Bahia (in which the São Francisco river has not acted as geographical barrier), Gr-Pernambuco, and Gr-Mato Grosso do Sul. The second included groups comprising populations of the states of Goiás, Tocantins, Minas Gerais, Bahia, São Paulo, and Espírito Santo. The mismatch distribution for groups was consistent with the model of demographic expansion, except for the Gr-Central-East_1 group. The diversification in this group occurred about 1.19 Mya during the Pleistocene, influenced by paleoclimatic oscillations during the Quaternary glacial cycles. [ABSTRACT FROM AUTHOR]

Tomato yellow leaf curl virus (TYLCV) causes great losses in tomato production. In addition to tomato, TYLCV infects many crops or weeds as alternative hosts. These alternative hosts may serve as reservoirs for TYLCV survival and spread. Here, we tested the capability of cultivated, flue-cured tobacco to act as a reservoir host plant for TYLCV. TYLCV DNA was detected in nine flue-cured tobacco cultivars inoculated with an infectious TYLCV clone, although no visible symptoms developed on TYLCV-infected tobacco plants. The percentage of whiteflies with viral DNA increased with an increasing acquisition access period (AAP) and reached 100% after a 12 h AAP on infected tobacco plants. Using infected tobacco plants as virus resources, TYLCV was capable of being transmitted to tobacco and tomato plants by whiteflies, and typical symptoms of TYLCV infection were observed on infected tomato plants but not on infected tobacco plants. Our results suggest that flue-cured tobacco can serve as a reservoir host plant for TYLCV and may play an important role in the spread of TYLCV epidemics in China. [ABSTRACT FROM AUTHOR]

Aneura pinguis is a thalloid liverwort species with broad geographical distribution. It is composed of cryptic species, however, the number of cryptic species within A. pinguis is not known. Five cpDNA regions (matK, rbcL, rpoC1, trnH-psbA and trnL-trnF) and the entire nuclear ITS region were studied in 130 samples of A. pinguis from different geographical regions. The relationships between the cryptic species of A. pinguis, A. maxima and A. mirabilis were analyzed. All of the examined samples were clustered into 10 clades corresponding to 10 cryptic species of A. pinguis (marked A to J). Aneura mirabilis and A. maxima were nested among different cryptic species of A. pinguis, which indicates that A. pinguis is a paraphyletic taxon. Subgroups were found in cryptic species A, B, C and E. As single barcodes, all tested DNA regions had 100% discriminant power and fulfilled DNA barcode criteria for species identification; however, the only combination detected in all subgroups was trnL-trnF with trnH-psbA or ITS2. The distances between cryptic species were 11- to 35-fold higher than intraspecific distances. In all analyzed DNA regions, the distances between most pairs of cryptic A. pinguis species were higher than between A. maxima and A. mirabilis. All cryptic species of A. pinguis clearly differed in their habitat preferences, which suggests that habitat adaptation could be the main driving force behind cryptic speciation within this taxon. [ABSTRACT FROM AUTHOR]

Sympatric divergent populations of the same species provide an opportunity to study the evolution and maintenance of reproductive isolation. Male mating calls are important in sexual selection in acoustically communicating species, and they also have the potential to maintain isolation among species or incipient species. We studied divergent south Indian populations of the bush cricket Mecopoda elongata which are extremely difficult to distinguish morphologically, but which exhibit striking divergence in male acoustic signals. We performed phonotactic experiments investigating the relative preference of females of the “Chirper” song type for calls of all 5 of the song types found in the region (in varying degrees of sympatry). We found that Chirper females preferred their own song type and were completely unresponsive to three trilling song types. Chirper females were occasionally attracted to the call type “Double Chirper” (the call most similar to their own type), suggesting call preference alone cannot provide a complete isolating mechanism. To investigate the basis of call preference we investigated the response of chirper females to variation in chirp rate. Chirper females responded most frequently to a mean chirp rate characteristic of their own song type rather than a higher chirp rate which would be more characteristic of the Double-Chirper song type. This suggests females drive stabilising selection on male chirp rate, which may contribute to the maintenance of isolation. Finally, a no-choice mating experiment using Chirper females and Chirper and Double Chirper males revealed a significant preference of Chirper females to mate with their own song type, even without a requirement for phonotaxis. Overall, the strong specificity of Chirper females for their ‘own’ song type provides evidence for behavioural isolation among divergent sympatric Mecopoda song types being maintained by female preference for both male song type and subsequent mating probability driven by other cues. [ABSTRACT FROM AUTHOR]

Mesalina are small lacertid lizards occurring in the Saharo-Sindian deserts from North Africa to the east of the Iranian plateau. Earlier phylogenetic studies indicated that there are several species complexes within the genus and that thorough taxonomic revisions are needed. In this study, we aim at resolving the phylogeny and taxonomy of the M. brevirostris species complex distributed from the Middle East to the Arabian/Persian Gulf region and Pakistan. We sequenced three mitochondrial and three nuclear gene fragments, and in combination with species delimitation and species-tree estimation, we infer a time-calibrated phylogeny of the complex. The results of the genetic analyses support the presence of four clearly delimited species in the complex that diverged approximately between the middle Pliocene and the Pliocene/Pleistocene boundary. Species distribution models of the four species show that the areas of suitable habitat are geographically well delineated and nearly allopatric, and that most of the species have rather divergent environmental niches. Morphological characters also confirm the differences between the species, although sometimes minute. As a result of all these lines of evidence, we revise the taxonomy of the Mesalina brevirostris species complex. We designate a lectotype for Mesalina brevirostris Blanford, 1874; resurrect the available name Eremias bernoullii Schenkel, 1901 from the synonymy of M. brevirostris; elevate M. brevirostris microlepis (Angel, 1936) to species status; and describe Mesalina saudiarabica, a new species from Saudi Arabia. [ABSTRACT FROM AUTHOR]

Aim Habitat specialization can constrain patterns of dispersal and drive allopatric speciation in organisms with limited dispersal ability. Herein, we tested biogeographic patterns and dispersal in a salamander with surface-dwelling larvae and obligate cave-dwelling adults. Location Ozark Plateau, eastern North America. Methods A population-level phylogeny of grotto salamanders ( Eurycea spelaea complex) was reconstructed using mitochondrial (mt DNA) and multi-locus nuclear DNA (nuc DNA), primarily derived from anchored hybrid enrichment ( AHE). We tested patterns of molecular variance among populations and associations between genetic distance and geographic features. Results Divergence time estimates suggest rapid formation of three major lineages in the Middle Miocene. Contemporary gene flow among divergent lineages appears negligible, and mt DNA suggests that most populations are isolated. There is a significant association between phylogenetic distance and palaeodrainages, contemporary drainages and sub-plateaus of the Ozarks, as all features explain a proportion of genetic variation. However, the greatest proportion of genetic variation is explained by the combined effects of palaeodrainages and sub-plateaus. Main conclusions The geologic and hydrologic history of the Ozark Plateau has influenced lineage diversification in the grotto salamander, leading to genetic isolation among populations. Limited gene flow and strong phylogeographic structure in this complex may result from the restriction of highly specialized adults to caves. [ABSTRACT FROM AUTHOR]

North America’s Great Basin has long been of interest to biologists due to its high level of organismal endemicity throughout its endorheic watersheds. One example of such a group is the subfamily Empetricthyinae. In this paper, we analyzed the relationships of the Empetrichtyinae and assessed the validity of the subspecies designations given by Williams and Wilde within the group using concatenated phylogenetic tree estimation and species tree estimation. Samples from 19 populations were included covering the entire distribution of the three extant species of Empetricthyinae–Crenichthys nevadae, Crenichthys baileyi and Empetricthys latos. Three nuclear introns (S8 intron 4, S7 intron 1, and P0 intron 1) and one mitochondrial gene (Cytb) were sequenced for phylogenetic analysis. Using these sequences, we generated two separate hypotheses of the evolutionary relationships of Empetrichtyinae- one based on the mitochondrial data and one based on the nuclear data using Bayesian phylogenetics. Haplotype networks were also generated to look at the relationships of the populations within Empetrichthyinae. After comparing the two phylogenetic hypotheses, species trees were generated using *BEAST with the nuclear data to further test the validity of the subspecies within Empetrichthyinae. The mitochondrial analyses supported four lineages within C. baileyi and 2 within C. nevadae. The concatenated nuclear tree was more conserved, supporting one clade and an unresolved polytomy in both species. The species tree analysis supported the presence of two species within both C. baileyi and C. nevadae. Based on the results of these analyses, the subspecies designations of Williams and Wilde are not valid, rather a conservative approach suggests there are two species within C. nevadae and two species within C. baileyi. No structure was found for E. latos or the populations of Empetricthyinae. This study represents one of many demonstrating the invalidity of subspecies and their detriment to species identification, conservation, and understanding. [ABSTRACT FROM AUTHOR]

Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%–9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail. [ABSTRACT FROM AUTHOR]

The diversity of free-living nematodes in the beaches of two Antarctic islands, King George and Deception islands was investigated. We used morphological and molecular (LSU, and two fragments of SSU sequences) approaches to evaluate 236 nematodes. Specimens were assigned to at least genera using morphology and were assessed for the presence of cryptic speciation. The following genera were identified: Halomonhystera, Litoditis, Enoploides, Chromadorita, Theristus, Oncholaimus, Viscosia, Gammanema, Bathylaimus, Choanolaimus, and Paracanthonchus; along with specimens from the families Anticomidae and Linhomoeidae. Cryptic speciation was identified within the genera Halomonhystera and Litoditis. All of the cryptic species identified live sympatrically. The two cryptic species of Halomonhystera exhibited no significant morphological differences. However, Litoditis species 2 was significantly larger than Litoditis species 1. The utility of molecular data in confirming the identifications of some of the morphologically more challenging families of nematodes was demonstrated. In terms of which molecular sequences to use for the identification of free-living nematodes, the SSU sequences were more variable than the LSU sequences, and thus provided more resolution in the identification of cryptic speciation. Finally, despite the considerable amount of time and effort required to put together genetic and morphological data, the resulting advance in our understanding of diversity and ecology of free-living marine nematodes, makes that effort worthwhile. [ABSTRACT FROM AUTHOR]

Tapeworms of the genus Anindobothrium Marques, Brooks & Lasso, 2001 are found in both marine and Neotropical freshwater stingrays of the family Potamotrygonidae. The patterns of host association within the genus support the most recent hypothesis about the history of diversification of potamotrygonids, which suggests that the ancestor of freshwater lineages of the Potamotrygonidae colonized South American river systems through marine incursion events. Despite the relevance of the genus Anindobothrium to understand the history of colonization and diversification of potamotrygonids, no additional efforts were done to better investigate the phylogenetic relationship of this taxon with other lineages of cestodes since its erection. This study is a result of recent collecting efforts to sample members of the genus in marine and freshwater potamotrygonids that enabled the most extensive documentation of the fauna of Anindobothrium parasitizing species of Styracura de Carvalho, Loboda & da Silva, Potamotrygon schroederi Fernández-Yépez, P. orbignyi (Castelnau) and P. yepezi Castex & Castello from six different countries, representing the eastern Pacific Ocean, Caribbean Sea, and river basins in South America (Rio Negro, Orinoco, and Maracaibo). The newly collected material provided additional specimens for morphological studies and molecular samples for subsequent phylogenetic analyses that allowed us to address the phylogenetic position of Anindobothrium and provide molecular and morphological evidence to recognize two additional species for the genus. The taxonomic actions that followed our analyses included the proposition of a new family, Anindobothriidae fam. n., to accommodate the genus Anindobothrium in the order Rhinebothriidea Healy, Caira, Jensen, Webster & Littlewood, 2009 and the description of two new species—one from the eastern Pacific Ocean, A. carrioni sp. n., and the other from the Caribbean Sea, A. inexpectatum sp. n. In addition, we also present a redescription of the type species of the genus, A. anacolum (Brooks, 1977) Marques, Brooks & Lasso, 2001, and of A. lisae Marques, Brooks & Lasso, 2001. Finally, we discuss the paleogeographical events mostly linked with the diversification of the genus and the protocols adopted to uncover cryptic diversity in Anindobothrium. [ABSTRACT FROM AUTHOR]

DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes. [ABSTRACT FROM AUTHOR]

Buergeria japonica is a widely distributed treefrog occurring from Ryukyu Archipelago to Taiwan. Across this wide distributional range, we combined molecular, acoustic, morphological, and behavioral characters to clarify the taxonomic status among these insular populations. Genetic differentiation in mitochondrial sequences indicated an over 16% divergence among two deeply divergent clades: Japanese clade distributes in Ryukyu Archipelago and northwestern drainages of Taiwan, while Taiwanese clade distributes in the remaining drainages on Taiwan. The Taiwanese clade can be distinguished from the nominative species not only by molecular and morphological differences, but also distinguishable by considerable acoustic differentiation, which is extraordinarily noticeable for an additional type of long call that never recorded from Japanese clade. The two clades form a parapatric distribution pattern with narrow contact zones both in western and eastern Taiwan. Playback experiments indicated that male frogs show significantly stronger defensiveness against conspecific calls rather than heterospecific calls, indicating that these signals play a crucial role in species recognition. Here we describe the Taiwanese clade as a new species; the behavioral response and the magnitude of gene flow across their contact zones are especially worth for detailed studies. [ABSTRACT FROM AUTHOR]

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification. [ABSTRACT FROM AUTHOR]

One of the most characteristic and abundant amphibian taxa of South American temperate forests is Eupsophus. The ten currently recognized species of the genus have been divided in two species groups, roseus and vertebralis, but most of them, eight, belong to the roseus group. Recent phylogeographic and phylogenetic studies have suggested that species diversity of the roseus group could be underestimated. An examination of the literature shows that species of the roseus group exhibit high levels of variation in their external characteristics, particularly those used as diagnostic characters, which compromises their taxonomy and hinders their field recognition. High levels of variation were also observed in several new populations of the roseus group discovered in southern Chile (36°-40°S), which could not be identified to the species level by their external characteristics. On the other hand, the literature reveals a scarse karyotype differentiation and a high bioacoustic uniformity among the species of the roseus group. We performed a Bayesian phylogenetic analysis using mitochondrial and nuclear genes to reevaluate the species diversity of the roseus group, including all the nominal species of Eupsophus and new populations. This analysis was complemented with three species delimitation approaches, General Mixed Yule Coalescent, multi-rate Poisson Tree Process and Automatic Barcode Gap Discovery. We favored a conservative delimitation of only four species for the roseus group, a result more consistent with the distribution of pairwise genetic distances, and the available chromosome and bioacoustic evidence. The four recognized lineages, which have nearly completely allopatric distributions, are named after the earliest nominal species that they include, but because high levels of phenotypic variation, they are not diagnosable by consistent differences in external morphology. We discuss the implications of this new proposal for the taxonomy and conservation of the genus, and the possible causes of the difficulty to estimate its species diversity. [ABSTRACT FROM AUTHOR]

The genus Glaucomys (New World flying squirrels) is currently considered to be comprised of 2 species, the northern flying squirrel (G. sabrinus) and the southern flying squirrel (G. volans). We synthesize new information from mitochondrial DNA (mtDNA) control region sequences and microsatellite data to demonstrate that the genus consists of 3, rather than 2 species, and that Glaucomys sabrinus, as currently recognized, is actually composed of 2 separate, apparently non-hybridizing species. Control region mtDNA data from 185 individuals across North America revealed 2 distinct clades embedded within G. sabrinus: a widespread "Continental" lineage and a more geographically restricted "Pacific Coastal" lineage. The geographic distributions of these 2 lineages are largely mutually exclusive, with sympatry observed at only 3 sites in the Pacific Northwest. Analysis of 8 microsatellite loci showed no evidence of hybridization between the 2 lineages of G. sabrinus in the region of sympatry. This lack of gene flow is noteworthy given that populations of the Continental lineage of G. sabrinus have been shown to hybridize with G. volans in southeastern Canada. Finally, phylogenetic analyses and estimates of divergence times show that G. volans and Continental G. sabrinus are actually sister taxa that diverged from one another more recently than either did from Pacific Coastal G. sabrinus. We propose that these observations provide strong evidence for a third, previously unrecognized species of North American flying squirrel, whose geographic range extends along the Pacific Coast from southern British Columbia to southern California. Glaucomys oregonensis (Bachman, 1839), whose type locality is in Oregon, is the senior available name for this taxon. We propose that this newly recognized species be given the common name "Humboldt's flying squirrel." [ABSTRACT FROM AUTHOR]

The Hajar Mountains of south-eastern Arabia form an isolated massif surrounded by the sea to the east and by a large desert to the west. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals. With 19 species restricted to the Hajar Mountains, reptiles are the vertebrate group with the highest level of endemicity, becoming an excellent model for understanding the patterns and processes that generate and shape diversity in this arid mountain range. The geckos of the Ptyodactylus hasselquistii species complex are the largest geckos in Arabia and are found widely distributed across the Arabian Mountains, constituting a very important component of the reptile mountain fauna. Preliminary analyses suggested that their diversity in the Hajar Mountains may be higher than expected and that their systematics should be revised. In order to tackle these questions, we inferred a nearly complete calibrated phylogeny of the genus Ptyodactylus to identify the origin of the Hajar Mountains lineages using information from two mitochondrial and four nuclear genes. Genetic variability within the Hajar Mountains was further investigated using 68 specimens of Ptyodactylus from 46 localities distributed across the entire mountain range and sequenced for the same genes as above. The molecular phylogenies and morphological analyses as well as niche comparisons indicate the presence of two very old sister cryptic species living in allopatry: one restricted to the extreme northern Hajar Mountains and described as a new species herein; the other distributed across the rest of the Hajar Mountains that can be confidently assigned to the species P. orlovi. Similar to recent findings in the geckos of the genus Asaccus, the results of the present study uncover more hidden diversity in the northern Hajar Mountains and stress once again the importance of this unique mountain range as a hot spot of biodiversity and a priority focal point for reptile conservation in Arabia. [ABSTRACT FROM AUTHOR]

Disentangling the role of competition in regulating the distribution of sympatric species can be difficult because species can have different habitat preferences or time use that introduce non-random patterns that are not related to interspecific interactions. We adopted a multi-step approach to systematically incorporate habitat preferences while investigating the co-occurrence of two presumed competitors, morphologically similar, and closely related ground-dwelling birds: the brown tinamou (Crypturellus obsoletus) and the tataupa tinamou (C. tataupa). First, we used single-species occupancy models to identify the main landscape characteristics affecting site occupancy, while accounting for detection probability. We then used these factors to control for the effect of habitat while investigating species co-occurrence. In addition, we investigated species present-time partitioning by measuring the degree of overlap in their activity time. Both species were strictly diurnal and their activity time highly overlapped (i.e., the species are not present-time partitioning). The distribution of the two species varied across the landscape, and they seemed to occupy opposite portions of the study area, but co-occurrence models and species interaction factors suggested that the tinamous have independent occupancy and detection. In addition, co-occurrence models that accounted for habitat performed better than models without habitat covariates. The observed co-occurrence pattern is more likely related to habitat preferences, wherein species segregated by elevation. These results provide evidence that habitat characteristics can play a bigger role than interspecific interactions in regulating co-existence of some species. Therefore, exploring habitat preferences while analyzing co-occurrence patterns is essential, in addition to being a feasible approach to achieve more accurate estimation of parameters reflecting species interactions. Occupancy models can be a valuable tool in such modeling. [ABSTRACT FROM AUTHOR]

Among the Oryzomyini (Sigmodontinae), Oecomys is the most speciose, with 17 species. This genus presents high karyotypic diversity (2n = 54 to 2n = 86) and many taxonomic issues at the species level because of the presence of cryptic species and the overlap of morphological characters. For these reasons the real number of species of Oecomys may be underestimated. With the aim of verifying if the taxon Oecomys catherinae is composed of more than one species, we made comparative studies on two populations from two regions of Brazil, one from the Amazon and another from the Atlantic Forest using both classical cytogenetics (G- and C-banding) and comparative genomic mapping with whole chromosome probes of Hylaeamys megacephalus (HME), molecular data (cytochrome b mitochondrial DNA) and morphology. Our results confirm that Oecomys catherinae occurs in the southeast Amazon, and reveal a new karyotype for the species (2n = 62, FNa = 62). The comparative genomic analysis with HME probes identified chromosomal homeologies between both populations and rearrangements that are responsible for the different karyotypes. We compared our results in Sigmodontinae genera with other studies that also used HME probes. These chromosomal differences together with the absence of consistent differentiation between the two populations on morphological and molecular analyses suggest that these populations may represent cryptic species. [ABSTRACT FROM AUTHOR]

Defining an acoustic repertoire is essential to understanding vocal signalling and communicative interactions within a species. Currently, quantitative and statistical definition is lacking for the vocalisations of many dasyurids, an important group of small to medium-sized marsupials from Australasia that includes the eastern quoll (Dasyurus viverrinus), a species of conservation concern. Beyond generating a better understanding of this species' social interactions, determining an acoustic repertoire will further improve detection rates and inference of vocalisations gathered by automated bioacoustic recorders. Hence, this study investigated eastern quoll vocalisations using objective signal processing techniques to quantitatively analyse spectrograms recorded from 15 different individuals. Recordings were collected in conjunction with observations of the behaviours associated with each vocalisation to develop an acoustic-based behavioural repertoire for the species. Analysis of recordings produced a putative classification of five vocalisation types: Bark, Growl, Hiss, Cp-cp, and Chuck. These were most frequently observed during agonistic encounters between conspecifics, most likely as a graded sequence from Hisses occurring in a warning context through to Growls and finally Barks being given prior to, or during, physical confrontations between individuals. Quantitative and statistical methods were used to objectively establish the accuracy of these five putative call types. A multinomial logistic regression indicated a 97.27% correlation with the perceptual classification, demonstrating support for the five different vocalisation types. This putative classification was further supported by hierarchical cluster analysis and silhouette information that determined the optimal number of clusters to be five. Minor disparity between the objective and perceptual classifications was potentially the result of gradation between vocalisations, or subtle differences present within vocalisations not discernible to the human ear. The implication of these different vocalisations and their given context is discussed in relation to the ecology of the species and the potential application of passive acoustic monitoring techniques. [ABSTRACT FROM AUTHOR]

The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina). Fisher occurrence records supported by physical evidence (verifiable records) were available from a limited area, whereas occurrence records of unknown quality (unscreened records) were available from throughout the fisher’s historical range. We reserved 20% of the verifiable records to use as a test sample for both models and generated SDMs with each dataset using Maxent. The verifiable model performed substantially better than the unscreened model based on multiple metrics including AUCtest values (0.78 and 0.62, respectively), evaluation of training and test gains, and statistical tests of how well each model predicted test localities. In addition, the verifiable model was consistent with our knowledge of the fisher’s habitat relations and potential distribution, whereas the unscreened model indicated a much broader area of high-quality habitat (indices > 0.5) that included large expanses of high-elevation habitat that fishers do not occupy. Because Pacific martens remain relatively common in upper elevation habitats in the Cascade Range and Sierra Nevada, the SDM based on unscreened records likely reflects primarily a conflation of marten and fisher habitat. Consequently, accurate identifications are far more important than the spatial extent of occurrence records for generating reliable SDMs for the fisher in this region. We strongly recommend that practitioners avoid using anecdotal occurrence records to build SDMs but, if such data are used, the validity of resulting models should be tested with verifiable occurrence records. [ABSTRACT FROM AUTHOR]

Polyps of two moon jellyfish species, Aurelia coerulea and A. relicta, from two Adriatic Sea coastal habitats were incubated under multiple combinations of temperature (14, 21°C), salinity (24, 37 ppt) and food regime (9.3, 18.6, 27.9 μg C ind−1 week−1) to comparatively assess how these factors may influence major asexual reproduction processes in the two species. Both species exhibited a shared pattern of budding mode (Directly Budded Polyps: DBP; Stolonal Budded Polyps: SBP), with DBP favoured under low food supply (9.3 μg C ind −1 week−1) and low temperature (14°C), and SBP dominant under high temperature (21°C). However, A. coerulea showed an overall higher productivity than A. relicta, in terms of budding and podocyst production rates. Further, A. coerulea exhibited a wide physiological plasticity across different temperatures and salinities as typical adaptation to ecological features of transitional coastal habitats. This may support the hypothesis that the invasion of A. coerulea across coastal habitats worldwide has been driven by shellfish aquaculture, with scyphistoma polyps and resting stages commonly found on bivalve shells. On the contrary, A. relicta appears to be strongly stenovalent, with cold, marine environmental optimal preferences (salinity 37 ppt, T ranging 14–19°C), corroborating the hypothesis of endemicity within the highly peculiar habitat of the Mljet lake. By exposing A. relicta polyps to slightly higher temperature (21°C), a previously unknown developmental mode was observed, by the sessile polyp regressing into a dispersive, temporarily unattached and tentacle-less, non-feeding stage. This may allow A. relicta polyps to escape climatic anomalies associated to warming of surface layers and deepening of isotherms, by moving into deeper, colder layers. Overall, investigations on species-specific eco-physiological and ontogenetic potentials of polyp stages may contribute to clarify the biogeographic distribution of jellyfish and the phylogenetic relationships among evolutionary related sister clades. [ABSTRACT FROM AUTHOR]

Cats are the most common mammal to develop invasive fungal rhinosinusitis caused by cryptic species in Aspergillus section Fumigati that are resistant to azoles but susceptible to caspofungin. In this study nonlinear mixed-effects pharmacokinetic modeling and simulation was used to investigate caspofungin pharmacokinetics and explore dosing regimens in cats using caspofungin minimum effective concentrations (MECs). Plasma concentrations in healthy cats were determined using HPLC-MS/MS after administration of a single and seven consecutive daily intravenous doses of 1 mg/kg caspofungin. In the final pharmacokinetic model an optimum maximum concentration (Cmax): MEC ratio of 10–20 was used to guide caspofungin efficacy. Simulations were performed for dosing regimens (doses 0.25–2 mg/kg and 6–72 h dosing intervals) with and without inclusion of a loading dose. Using a 1 mg/kg dose Cmax first dose was 14.8 μg/mL, Cmax at steady state was 19.8 μg/mL, Cmin was 5 μg/mL and Cmax: MEC was >20 in 42.6% of cats after multiple doses. An optimal Cmax: MEC ratio was achieved in caspofungin simulations using 0.75 mg/kg q 24 h or 1 mg/kg q 72h. However, at 1 mg/kg q 72h, Cmin was < MEC (<1 μg/mL) in over 95% of the population. Using a loading dose of 1 mg/kg and a daily dose of 0.75 mg/kg thereafter, the Cmax: MEC was optimal and Cmin was > 2.5 μg/mL for 98% of the population. Based on the modeling data this dosing regimen is likely to achieve target therapeutic concentrations, meet the proposed Cmax: MEC window and provide consistent exposure between doses. [ABSTRACT FROM AUTHOR]

The mosquito family (Diptera: Culicidae) constitutes the most medically important group of arthropods because certain species are vectors of human pathogens. In some parts of the world, the diversity is so high that the accurate delimitation and/or identification of species is challenging. A DNA-based identification system for all animals has been proposed, the so-called DNA barcoding approach. In this study, our objectives were (i) to establish DNA barcode libraries for the mosquitoes of French Guiana based on the COI and the 16S markers, (ii) to compare distance-based and tree-based methods of species delimitation to traditional taxonomy, and (iii) to evaluate the accuracy of each marker in identifying specimens. A total of 266 specimens belonging to 75 morphologically identified species or morphospecies were analyzed allowing us to delimit 86 DNA clusters with only 21 of them already present in the BOLD database. We thus provide a substantial contribution to the global mosquito barcoding initiative. Our results confirm that DNA barcodes can be successfully used to delimit and identify mosquito species with only a few cases where the marker could not distinguish closely related species. Our results also validate the presence of new species identified based on morphology, plus potential cases of cryptic species. We found that both COI and 16S markers performed very well, with successful identifications at the species level of up to 98% for COI and 97% for 16S when compared to traditional taxonomy. This shows great potential for the use of metabarcoding for vector monitoring and eco-epidemiological studies. [ABSTRACT FROM AUTHOR]

Aphids are major pests of cereal crops and a suite of hymenopteran primary parasitoids play an important role in regulating their populations. However, hyperparasitoids may disrupt the biocontrol services provided by primary parasitoids. As such, understanding cereal aphid-primary parasitoid-hyperparasitoid interactions is vital for a reliable parasitoid-based control of cereal aphids. For this, the ability to identify the different primary and hyperparasitoid species is necessary. Unfortunately, this is often difficult due to a lack of morphologically diagnostic features. DNA sequence-based species identification of parasitoids can overcome these hurdles. However, comprehensive DNA sequence information is lacking for many of these groups, particularly for hyperparasitoids. Here we evaluate three genes [cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S) and 18S ribosomal RNA (18S)] for their suitability to identify 24 species of primary parasitoids and 16 species of hyperparasitoids associated with European cereal aphids. To identify aphelinid primary parasitoid species and hyperparasitoids, we found 16S to be more suitable compared to COI sequences. In contrast, the Aphidiinae are best identified using COI due to better species-level resolution and a more comprehensive DNA sequence database compared to 16S. The 18S gene was better suited for group-specific identification of parasitoids, but did not provide resolution at the species level. Our results provide a DNA sequence database for cereal aphid primary parasitoids and their associated hyperparasitoids in Central Europe, which will allow further improvement of our understanding of cereal aphid-primary parasitoid-hyperparasitoid interactions in relation to aphid biological control. [ABSTRACT FROM AUTHOR]