Decoding of superimposed traces produced by direct sequencing of heterozygous indels

PolyQ Length of the Clock Gene Is Correlated With Pelagic Larval Duration in the Damselfishes (Pomacentridae), but Within a Species Habitat Availability Counts

Immediately after hatching, larvae of coral reef fish leave their natal reef environment and begin their pelagic larval phase probably to avoid high predation on the reef. The time they spend in the open ocean (pelagic larval duration, PLD), before settlement varies from species to species and depends partly on developmental processes that eventually require re-settlement to a reef. The polyglutamine region (PolyQ) as part of the clock gene has been suggested as a possible candidate that could control developmental processes and potentially the time until settlement, which can be determined by counting the rings of the otoliths. We studied the potential relationship between the number of glutamine repeats in 20 species of pomacentrids and their PLDs. Most pomacentrids came from similar locations, so we avoided the impact of latitudinal clines on PLD. Within the clock gene, we found two main distinguishable, variable glutamine-rich regions (PolyQ and Qrich). Considering phylogenetic relationships, PolyQ/Qrich repeat length and pelagic larval duration were significantly positively correlated. However, when analyzing this relationship in a single species, the neon damselfish (Pomacentrus coelestis), we did not find a significant correlation between PolyQ length variation and PLD. Instead, we found a significant reduction of PLD in years with increased habitat availability. Our results show that glutamine-rich regions can influence the timing of settlement on a broader scale, but that ecological factors-such as habitat availability-can also have a significant impact.

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest

Background

The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex.

Methods

We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations.

Results

Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.

A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines

The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.

Double trouble: untangling mixed sequence signals in bird samples with avian haemosporidian co-infections

Blood parasites comprise some of the most prevalent pathogens in nature, and their detection and identification are major objectives in varied fields such as ecology and biomedicine. Two approaches were compared, one based on Sanger sequencing and the other next-generation sequencing (NGS) based, in terms of their performance in detecting avian blood parasites across tropical Southeast Asian birds. Across a panel of 528 bird individuals, 43 birds were ascertained to be infected with avian haemosporidians using a polymerase chain reaction-based detection method. Among these samples, NGS-based barcoding confirmed co-infections by multiple blood parasites in all eight cases where Sanger sequencing produced double peaks. Importantly however, the NGS-based method produced another five diagnoses of co-infections (62.5%) in which Sanger-based barcoding remained equivocal. In contrast to Sanger sequencing, the NGS-based method was able to identify co-infecting haemosporidian lineages via their barcodes. The accuracy of avian haemosporidian lineage identification was not compromised by the shorter length of NGS sequences, with ~94% of NGS barcodes producing matches identical to those of the Sanger barcodes. The application of NGS-based barcoding methods promises to enhance parasite identification and reduce erroneous inferences based on artefacts.

Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants

Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.

Inference of CRISPR Edits from Sanger Trace Data

Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.

Significance of incongruent DNA loci in the taxonomy of wood-decaying Basidioradulum radula

Modern taxonomic studies of Agaricomycetes rely on the integrative analyses of morphology, environmental data, geographic distribution, and usually several DNA loci. However, sampling and selection of DNA loci for the analyses are commonly shallow. In this study, we suggest minimal numbers of necessary specimens to sample and DNA loci to analyze in order to prevent inadequate taxonomic decisions in species groups with minor morphological and genealogical differences. We sampled four unlinked nuclear DNA gene regions (nuc rDNA ITS1-5.8S-ITS2, gh63, rpb2, and tef1) to revise the systematics of a common wood-decaying species Basidioradulum radula (Hymenochaetales) on an intercontinental set of specimens collected in the Northern Hemisphere. The DNA loci analyzed violate the genealogical concordance phylogenetic species recognition principles, thus confirming a single-species interpretation. We conclude that Hyphodontia syringae is a younger synonym of B. radula.

CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification

Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3% (428/431) and 95.1% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.

Convergent evolution of pain-inducing defensive venom components in spitting cobras

Convergent evolution provides insights into the selective drivers underlying evolutionary change. Snake venoms, with a direct genetic basis and clearly defined functional phenotype, provide a model system for exploring the repeated evolution of adaptations. While snakes use venom primarily for predation, and venom composition often reflects diet specificity, three lineages of cobras have independently evolved the ability to spit venom at adversaries. Using gene, protein, and functional analyses, we show that the three spitting lineages possess venoms characterized by an up-regulation of phospholipase A2 (PLA2) toxins, which potentiate the action of preexisting venom cytotoxins to activate mammalian sensory neurons and cause enhanced pain. These repeated independent changes provide a fascinating example of convergent evolution across multiple phenotypic levels driven by selection for defense.

Darwin Returns to the Galapagos: Genetic and Morphological Analyses Confirm the Presence of Tramea darwini at the Archipelago (Odonata, Libellulidae)

The status of the Tramea species present in the Galapagos Islands (Odonata, Libellulidae) has been the subject of a long-standing debate among odonatologists. Here, we use molecular and morphological data to analyze a series of specimens from this genus collected in 2018 from the Islands of San Cristobal, Isabela, and Santa Cruz, with the aim of determining their relationship with Tramea calverti Muttkowski and with their currently considered senior synonym T. cophysa Hagen. We combined sequencing of mitochondrial and nuclear DNA with morphological examination of several specimens of Tramea, including representatives of continental T. cophysa and T. calverti. Our molecular analyses place the Tramea from Galapagos in the same clade as T. calverti, with T. cophysa as a closely related species. The morphological analyses found only one consistent difference between T. cophysa and T. calverti: the presence of an accessory lobe in the male vesica spermalis of T. cophysa that is absent in T. calverti and in the Tramea from Galapagos. In agreement with our genetic results, the overall morphological differences documented by us indicate that the Galapagos material examined is conspecific with T. calverti. In light of this, and following the principle of priority in taxonomic nomenclature, Tramea calverti Muttkowski, 1910 should hereafter be considered a junior synonym of Tramea darwini Kirby, 1889.

Evidence of introgression in endemic frogs from the campo rupestre contradicts the reduced hybridization hypothesis

The campo rupestre ecosystem is considered an old, climatically buffered, infertile landscape. As a consequence, long-term isolation is thought to have played an important role in the diversification of its biota. Here, we tested for hybridization between two endemic leaf frogs from the campo rupestre. We used sequence markers and coalescent models to verify haplotype sharing between the species, to test the existence and direction of gene flow, and to reconstruct the spatiotemporal dynamics of gene flow. Additionally, ecological niche modelling (ENM) was used to assess for potential co-occurrence by overlapping the climatic niche of these species since the middle Pleistocene. We found haplotype sharing and/or lack of differentiation in four nuclear fragments, one of them associated with introgression. The coalescent models support introgressive hybridization unidirectionally from Pithecopus megacephalus to P. ayeaye, occurring ~300 kya. ENM corroborates this scenario, revealing areas of potential environmental niche overlap for the species at about 787 kya. These results contradict the expectation of reduced hybridization, while ENM suggests climatic fluctuation rather than stability for the two species. The reduced hybridization hypothesis needs to be further investigated because our results suggest that it may have unrealistic premises at least for animals.

New Genetic Insights About Hybridization and Population Structure of Hawksbill and Loggerhead Turtles From Brazil

An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. This atypical phenomenon and its impact on sea turtle conservation can be elucidated through research focused on the evolutionary history of sea turtles. We assessed high-quality multilocus haplotypes of 143 samples of the 5 species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill × loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation

Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification among clades. However, why the climatic niche evolves more rapidly in some clades than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among species with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among species.

Widespread Wolbachia infection in an insular radiation of damselflies (Odonata, Coenagrionidae)

Wolbachia is one of the most common endosymbionts found infecting arthropods. Theory predicts symbionts like Wolbachia will be more common in species radiations, as host shift events occur with greatest frequency between closely related species. Further, the presence of Wolbachia itself may engender reproductive isolation, and promote speciation of their hosts. Here we screened 178 individuals belonging to 30 species of the damselfly genera Nesobasis and Melanesobasis - species radiations endemic to the Fiji archipelago in the South Pacific - for Wolbachia, using multilocus sequence typing to characterize bacterial strains. Incidence of Wolbachia was 71% in Nesobasis and 40% in Melanesobasis, and prevalence was also high, with an average of 88% in the Nesobasis species screened. We identified a total of 25 Wolbachia strains, belonging to supergroups A, B and F, with some epidemic strains present in multiple species. The occurrence of Wolbachia in both males and females, and the similar global prevalence found in both sexes rules out any strong effect of Wolbachia on the primary sex-ratio, but are compatible with the phenotype of cytoplasmic incompatibility. Nesobasis has higher species richness than most endemic island damselfly genera, and we discuss the potential for endosymbiont-mediated speciation within this group.

Late Pleistocene climatic changes promoted demographic expansion and population reconnection of a Neotropical savanna-adapted bird, Neothraupis fasciata (Aves: Thraupidae)

We performed phylogeographic and genetic structure analyses of Neothraupis fasciata joined with species distribution modelling to evaluate whether: (1) the distribution of genetic variability shows a pattern expected by the isolation-by-distance model; (2) the influence of the Pleistocene climate changes on species distribution; and (3) climate/climatic stability (hypothesis of climatic stability) as a predictor of population genetic diversity. Based on two molecular datasets (ND2 and FIB-5), the isolation-by-distance hypothesis was not supported. The mitochondrial haplotype network indicated the existence of historically isolated populations at the southern range of the species distribution, and recent population expansion was identified by both neutrality tests and extended Bayesian skyline plot analysis. Thus, the climatic changes during the Pleistocene might have promoted the reconnection of the partially isolated southern populations, which may have persisted in the plateaus during the cycles of savanna contractions. Subsequently, this species (re)colonized northern areas of the species present distribution, following the continuous vegetation on the São Francisco and Central plateaus about 60 kyr, and also reached the Amazonian savannas likely via the central corridor. Thus, our results indicated that the intrinsic relationship between the relief heterogeneity (plateaus and depressions) and the climatic fluctuations, mainly in the Pleistocene, promoted population reconnection and demographic expansion of N. fasciata.

Genome Editing in Mouse Embryos with CRISPR/Cas9

Transgenic mouse models can be subdivided into two main categories based on genomic location: (1) targeted genomic manipulation and (2) random integration into the genome. Despite the potential confounding insertional mutagenesis and host locus-dependent expression, random integration transgenics allowed for rapid in vivo assessment of gene/protein function. Since precise genomic manipulation required the time-consuming prerequisite of first generating genetically modified embryonic stem cells, the rapid nature of generating random integration transgenes remained a strong benefit outweighing various disadvantages. The advent of targetable nucleases, such as CRISPR/Cas9, has eliminated the prerequisite of first generating genetically modified embryonic stem cells for some types of targeted genomic mutations. This chapter outlines the generation of mouse models with targeted genomic manipulation using the CRISPR/Cas9 system directly into single cell mouse embryos.

First steps towards assessing the evolutionary history and phylogeography of a widely distributed Neotropical grassland bird (Motacillidae: Anthus correndera)

Grasslands in southern South America are extensive ecosystems which harbor a unique biodiversity; however, studies on the evolution of their taxa are scarce. Here we studied the phylogeography and population history of the Correndera Pipit (Anthus correndera), a grassland specialist bird with a large breeding distribution in southern South America, with the goals of investigating its phylogeographic history and relate it to the historical development of South American grasslands. The mitochondrial NADH dehydrogenase subunit II gene (ND2) was sequenced in 66 individuals from 19 localities and the intron 9 of the sex-linked gene for aconitase (ACOI9) was sequenced from a subset of those individuals, including all five subspecies of A. correndera, as well as the closely related A. antarcticus. Phylogenetic analysis revealed two distinct lineages within the complex: the first (A) corresponding to Andean subspecies A. c. calcaratus and A. c. catamarcae and the second (B) including birds traditionally assigned to A. c. correndera, A. c. chilensis, A. c. grayi and some individuals of A. c. catamarcae. A. antarcticus is nested within this second lineage. These results were also supported by evidence of niche divergence for variables associated with precipitation. The oldest split between clade A and B was estimated at c. 0.37 Mya, during the middle Pleistocene. Species distribution models for the present and the Last Glacial Maximum (LGM) suggest that grassland areas in southern South America remained relatively stable, in contrast to the general view of a reduction in grassland cover in South America since the LGM. Recent divergences and low phylogeographic structure (for lowland vs. highland geographic groups, intra-population genetic variance was greater than inter-groups; e.g., for ACOI9: 95.47% and ND2: 51.51% respectively), suggest widespread gene flow between lowland populations.

Limited introgression supports division of giraffe into four species

All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi-locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here, we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings support a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, and mostly occurring in politically unstable regions, and as such, require the highest conservation support possible.

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4-6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones

The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc.

Evolutionarily significant units of the critically endangered leaf frog Pithecopus ayeaye (Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network

Protected areas (PAs) are essential for biodiversity conservation, but their coverage is considered inefficient for the preservation of all species. Many species are subdivided into evolutionarily significant units (ESUs) and the effectiveness of PAs in protecting them needs to be investigated. We evaluated the usefulness of the Brazilian PAs network in protecting ESUs of the critically endangered Pithecopus ayeaye through ongoing climate change. This species occurs in a threatened mountaintop ecosystem known as campos rupestres. We used multilocus DNA sequences to delimit geographic clusters, which were further validated as ESUs with a coalescent approach. Ecological niche modeling was used to estimate spatial changes in ESUs' potential distributions, and a gap analysis was carried out to evaluate the effectiveness of the Brazilian PAs network to protect P. ayeaye in the face of climate changes. We tested the niche overlap between ESUs to gain insights for potential management alternatives for the species. Pithecopus ayeaye contains at least three ESUs isolated in distinct mountain regions, and one of them is not protected by any PA. There are no climatic niche differences between the units, and only 4% of the suitable potential area of the species is protected in present and future projections. The current PAs are not effective in preserving the intraspecific diversity of P. ayeaye in its present and future range distributions. The genetic structure of P. ayeaye could represent a typical pattern in campos rupestres endemics, which should be considered for evaluating its conservation status.

A possible origin population of pathogenic intestinal nematodes, Strongyloides stercoralis, unveiled by molecular phylogeny

Humans and dogs are the two major hosts of Strongyloides stercoralis, an intestinal parasitic nematode. To better understand the phylogenetic relationships among S. stercoralis isolates infecting humans and dogs and to assess the zoonotic potential of this parasite, we analyzed mitochondrial Cox1, nuclear 18S rDNA, 28S rDNA, and a major sperm protein domain-containing protein genes. Overall, our analyses indicated the presence of two distinct lineages of S. stercoralis (referred to as type A and type B). While type A parasites were isolated both from humans and dogs in different countries, type B parasites were found exclusively in dogs, indicating that the type B has not adapted to infect humans. These epidemiological data, together with the close phylogenetic relationship of S. stercoralis with S. procyonis, a Strongyloides parasite of raccoons, possibly indicates that S. stercoralis originally evolved as a canid parasite, and later spread into humans. The inability to infect humans might be an ancestral character of this species and the type B might be surmised to be an origin population from which human-infecting strains are derived.

How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas

Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.

Genetic structure of coral-Symbiodinium symbioses on the world's warmest reefs

Corals in the Arabian/Persian Gulf (PAG) survive extreme sea temperatures (summer mean: >34°C), and it is unclear whether these corals have genetically adapted or physiologically acclimated to these conditions. In order to elucidate the processes involved in the thermal tolerance of PAG corals, it is essential to understand the connectivity between reefs within and outside of the PAG. To this end, this study set out to investigate the genetic structure of the coral, Platygyra daedalea, and its symbiotic algae in the PAG and neighbouring Gulf of Oman. Using nuclear markers (the ITS region and an intron of the Pax-C gene), this study demonstrates genetic divergence of P. daedalea on reefs within the thermally extreme PAG compared with those in the neighbouring Gulf of Oman. Isolation by distance of P. daedalea was supported by the ITS dataset but not the Pax-C intron. In addition, the symbiont community within the PAG was dominated by C3 symbionts, while the purportedly thermotolerant clade D was extremely rare and was common only at sites outside of the PAG. Analysis of the psbA^ncr indicates that the C3 variant hosted by P. daedalea in the PAG belongs to the newly described species, Symbiodinium thermophilum. The structuring of the coral and symbiont populations suggests that both partners of the symbiosis may contribute to the high bleaching thresholds of PAG corals. While limited gene flow has likely played a role in local adaptation within the PAG, it also indicates limited potential for natural export of thermal tolerance traits to reefs elsewhere in the Indian Ocean threatened by climate change.

Histone methyltransferase Setd2 is critical for the proliferation and differentiation of myoblasts

Skeletal muscle cell proliferation and differentiation are tightly regulated. Epigenetic regulation is a major component of the regulatory mechanism governing these processes. Histone modification is part of the epigenetic code used for transcriptional regulation of chromatin through the establishment of an active or repressive state for genes involved in myogenesis in a temporal manner. Here, we uncovered the function of SET domain containing 2 (Setd2), an essential histone 3 lysine 36 trimethyltransferase, in regulating the proliferation and differentiation of myoblasts. Setd2 was silenced in the skeletal muscle myoblast cell line, C2C12, using the CRISPR/CAS9 system. The mutant cells exhibited defect in myotube formation. The myotube formation marker, myosin heavy chain (MHC), was downregulated earlier in Setd2 silenced cells compared to wild-type myoblasts during differentiation. The deficiency in Setd2 also resulted in repression of Myogenin (MyoG) expression, a key myogenic regulator during differentiation. In addition to the myoblast differentiation defect, decreased proliferation rate with significantly reduced levels of histone 3 phosphorylation, indicative of cell proliferation defect, were observed in the Setd2 silenced cells; suggesting an impaired proliferation phenotype. Furthermore, compromised G1/S- and G2/M-phase transition and decreased expression levels of major regulators of cell cycle G1/S checkpoints, cyclin D1, CDK4, CDK6, and cyclin E2 were detected in Setd2 silenced cells. Consistent with the cell cycle arrested phenotype, cyclin-dependent kinase inhibitor p21 was upregulated in Setd2 silenced cells. Together, this study demonstrates an essential role of Setd2 in myoblast proliferation and differentiation, and uncovers Setd2-mediated molecular mechanism through regulating MyoG and p21.

Multilocus Intron Trees Reveal Extensive Male-Biased Homogenization of Ancient Populations of Chamois (Rupicapra spp.) across Europe during Late Pleistocene

The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.

CRISP-ID: decoding CRISPR mediated indels by Sanger sequencing

The advent of next generation gene editing technologies has revolutionized the fields of genome engineering in allowing the generation of gene knockout models and functional gene analysis. However, the screening of resultant clones remains challenging due to the simultaneous presence of different indels. Here, we present CRISP-ID, a web application which uses a unique algorithm for genotyping up to three alleles from a single Sanger sequencing trace, providing a robust and readily accessible platform to directly identify indels and significantly speed up the characterization of clones.

Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico

Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter- and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A₂ such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved.

Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells

CRISPR/Cas9 nuclease systems can create double-stranded DNA breaks at specific sequences to efficiently and precisely disrupt, excise, mutate, insert, or replace genes. However, human embryonic stem or induced pluripotent stem cells (iPSCs) are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe an optimized protocol for genome engineering of human iPSCs using a simple transient transfection of plasmids and/or single-stranded oligonucleotides. With this protocol, we achieve transfection efficiencies greater than 60%, with gene disruption efficiencies from 1-25% and gene insertion/replacement efficiencies from 0.5-10% without any further selection or enrichment steps. We also describe how to design and assess optimal sgRNA target sites and donor targeting vectors; cloning individual iPSC by single cell FACS sorting, and genotyping successfully edited cells.

CRISPRing into the woods

The CRISPR/Cas9 technology is a welcome breakthrough for genome editing, owing to its precision, efficiency, versatility and ease of adoption. We recently reported the first application of CRISPR/Cas9 for biallelic mutations in stably transformed Populus, extending the species range of this powerful technology to woody perennials. An underappreciated obstacle in genome editing of outcrossing species is the frequent occurrence of sequence polymorphisms that can render CRISPR/Cas9 unproductive. We discuss experimental evidence as well as genome-wide computational analysis to demonstrate the sensitivity of CRISPR/Cas9 to allelic heterozygosity, and highlight tools and strategies that can help deal with such sequence polymorphisms. With its specificity, CRISPR/Cas9 offers a less equivocal means than previous approaches for discerning functional redundancy of paralogous genes that are prevalent in plant genomes. Continuing improvements of the CRISPR/Cas9 system for multiplex genome engineering should facilitate these efforts. The paradigm shift brought about by CRISPR/Cas9 promises to accelerate not only basic research but also applied crop improvement progress.

High levels of genetic connectivity among populations of yellowtail snapper, Ocyurus chrysurus (Lutjanidae-Perciformes), in the western South Atlantic revealed through multilocus analysis

In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans.