Cryptic Species Research Articles

Comparative transcriptome analysis of whiteflies raised on cotton leaf curl Multan virus-infected cotton plants.

Cotton leaf curl Multan virus (CLCuMuV), a serious viral disease causative agent in cotton plants in South Asia, is transmitted by the Bemisia tabaci cryptic species complex in a persistent circulative manner. A previous study indicated that Asia II-7 whiteflies could transmit CLCuMuV, while Mediterranean (MED) whiteflies failed to transmit CLCuMuV. However, little is known about the genes involved in this process. In this study, Asia II-7 and MED B. tabaci were utilized to determine transcriptomic responses after 48 h of acquisition access periods (AAPs). Result of Illumina sequencing revealed that, 14,213 and 8,986 differentially expressed genes (DEGs) were identified. Furthermore, DEGs related to the immune system and metabolism of Asia II-7 and MED in response to CLCuMuV-infected plants were identified and analyzed using Gene Ontologies (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the number of related DEGs in MED was lower than that of Asia II-7. The most abundant groups of DEGs between both viruliferous and aviruliferous whitefly species were the zf-C2H2 family of transcription factors (TFs). Notably, in comparison to viruliferous MED, Asia II-7 exhibited more DEGs related to cathepsin biosynthesis. Overall, this study provides the basic information for investigating the molecular mechanism of how begomoviruses affect B. tabaci metabolism and immune response either as vector cryptic species or non-vector species.

A new species of yellow acorn ant discovered in Italy via integrative taxonomy (Temnothorax luteus-complex, Formicidae)

The Mediterranean, a global hotspot for rare ant species, hosts a significant representation of the global diversity of the mainly Holarctic ant genus Temnothorax. However, several groups still require significant taxonomic efforts. The taxonomy of the T. luteus complex species was revised in 2014 when morphometrics allowed distinguishing two valid species and two synonyms out of four taxa that had been originally described from France. The two species recognized since then are T. luteus, distributed from Iberia to the Alps, and the largely sympatric but much more xerothermophilic T. racovitzai. In Italy, only a few records of the complex were ever published, and the identity of the Italian population was never thoroughly assessed. We combined morphometrics with phylogenomic data to assess the identity of the T. luteus populations that spanned from Sicily to the Italian Alps and discovered that all Italian samples belong to a new cryptic species, which we describe as T. apenninicussp. nov. whose glacial refugium was probably in the southern Apennines.

RCR-RFLP approach for identification of cryptic species of Bombus lucorum-complex in Northern European Russia

RCR-RFLP approach for identification of cryptic species of Bombus lucorum-complex in Northern European Russia

Invasive aspergillosis due to cryptic Aspergillus species: A prospective study from a single centre in India

Background& objective: The existence of visually identical cryptic Aspergillus species that can be distinguished only by molecular techniques is becoming more widely acknowledged. For the majority of antifungal drugs, these are known to exhibit a greater minimal inhibitory concentration in vitro. For the purpose of receiving the proper care, it is crucial to identify these species at right time. Our aim in this work is to identify and describe the Aspergillus species that are cryptic from all of the clinical samples. MethodsRoutine samples from inpatients and outpatients received in department of Microbiology, All India Institute of Medical Sciences, New Delhi, showing growth of Aspergillus species were included in this study. Phenotypic and Matrix Assisted Laser Desorption Ionisation - Time of Flight identified isolates were analysed for cryptic species, by PCR and ITS/ß – tubulin sequencing. In accordance with CLSI recommendations, antifungal susceptibility testing was conducted using micro broth dilution. ResultsOf the 94 isolates, 54 A. fumigatus, 34 A. flavus, 3 A. nidulans, 2 A. terreus, and 1 A. niger were morphologically identified. MALDI-TOF misidentified 2 A. nidulans isolates and 1 A, stellatus isolate. The ß – tubulin sequence analysis revealed that 2 isolates (2.08 %) were cryptic, one was A. stellatus and another one was A. tubingensis.

Everywhere we look around: Aerial eDNA to capture fungal diversity

AbstractResearch Highlight discussing: Runnel, K., Lõhmus, P., Küngas, K., Marmor‐Ohtla, L., Palo, A., Pütsepp, G., Tamm, H., Tammekänd, I., & Lõhmus, A. (2024). Aerial eDNA contributes vital information for fungal biodiversity assessment. Journal of Applied Ecology, https://doi.org/10.1111/1365‐2664.14691. Fungi play key roles in ecosystems, yet it is not clear how best to capture their diversity or monitor their presence, especially for those species of particular conservation concern. In this issue of the Journal of Applied Ecology Runnel et al. address this problem by comparing different methodologies to estimate the diversity of lichen‐forming fungi and wood‐inhabiting basidiomycetes at a forest stand scale. Pairing aerial eDNA sampling with visual observation‐based surveys better captured the full spectrum of fungal diversity, including cryptic species and those of particular conservation interest. Certain fungal groups that are underrepresented in air samples might be better captured by sampling eDNA directly from wood or soil, but visual surveys should be considered as a more cost‐effective complementary method at least at a local scale. Their results highlight the importance of using multiple methods simultaneously in biodiversity assessments and the need for standardized methods to study and monitor fungal diversity.

Phylogenetic systematics and integrative taxonomy contribute to weed biological control

Taxonomy and systematics are at the base of any biological research, providing the scientific names and evolutionary context to access the biological information needed. The biological control of weeds (BCW), like many other fields, often suffers from the “taxonomic impediment” generated by incomplete taxonomic knowledge or lack of available taxonomic experts on the particular taxa involved (i.e., weed plants and their potential biocontrol agents). Further, most groups with described species require revision by specialists using modern taxonomic methods. Systematists in the different taxonomic groups have the knowledge and experience to perform the accurate identification of the species involved in the study, to recognize if they are non-native species, or if they are new to science. Their expertise is crucial for identifying the organisms involved in BCW, including hybrids or cryptic species. The practice of phylogenetic systematics allows the discovery of evolutionary relationships and natural taxa that are valuable in making host range predictions. This contribution emphasizes the crucial role played by phylogenetic systematics and integrative taxonomy in weed biological control.

Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii.

Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25-75.4 Mb), were ∼8 Mb larger than the B. dermatitidis genomes (64.88-66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the two species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04-39.26 Mb) than in B. dermatitidis (30.85-32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation and speciation, highlighting the role of transposable elements in fungal evolution.

Exploring Bemisia tabaci Middle East-Asia Minor I and Mediterranean Cryptic Species Relationship with Cowpea Mild Mottle Virus and Their Dynamics in Soybean Fields.

Cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexividae) is an economically important virus infecting soybeans in Brazil, where it was initially identified in 1983. CPMMV is transmitted by the whitefly, Bemisia tabaci, and occasionally by seeds. Over the last three decades, the most invasive B. tabaci Middle East-Asia Minor 1 (MEAM1), and lately the Mediterranean (MED) cryptic species, have replaced the indigenous species in Brazil, with MEAM1 being predominant. In this study, we investigated the transmission properties of CPMMV by MEAM1 and MED, and their distribution in major soybean-growing areas in São Paulo State. Our results from transmission assays with a single insect revealed that MED is a more efficient vector compared to MEAM1, transmitting the virus within a two-minute inoculation access period. B. tabaci MEAM1 is still the predominant whitefly species in São Paulo State, but MED was also identified in different places, mainly in mixed infestations with MEAM1. Some areas transitioned to a predominance of MED over the three years, while others, where MED had previously been detected, showed a reduction in the insects during the same period. Understanding the transmission dynamics of CPMMV and the distribution of its vectors is crucial for implementing effective management strategies to control the virus spread and protect soybean crops. Further research into the mechanisms driving the shifts in whitefly species dominance and CPMMV distribution will be essential for sustaining soybean production in Brazil.

A phylogeographic approach to Sulawesi’s Maros karst shrimp fauna (Decapoda, Atyidae) reveals several cave invasions and challenges current taxonomic hypotheses

Abstract The unique endemic cave fauna of the Maros karst cave system (Sulawesi, Indonesia) includes atyid freshwater shrimps only known from their species descriptions. An extensive survey revealed a total of ten species in epigean and subterranean rivers: Two non-endemic, four species endemic to Sulawesi (genus Caridina) and four stygobiont species (genus Caridina, Marosina, and Parisia) only endemic to the Maros karst. A molecular phylogeny revealed (1) two independent colonizations of Sulawesi’s Maros karst caves by species of Caridina (Clade 1) derived from endemic ancestors, and (2) an exclusively stygobiont group (Clade 2, Marosina, Parisia) possibly derived from an amphidromous, anchialine cave-dweller. Our approach revealed another cryptic cave species of Caridina and challenges the taxonomic status of four Sulawesi endemics. In conclusion, the freshwater shrimps of the Maros karst are a challenging but rewarding group that can contribute to our understanding of the evolution of cave-dwelling species and atyid phylogenetics.

Combined Effects of Local and Regional Drivers on Oyster Spat Density and Growth in Eastern Australia

Up to 85% of shellfish reefs have been lost worldwide, resulting in declining ecosystem services, and increasing restoration demand. However, more information regarding the conditions which maximise oyster settlement and growth is required to optimise restoration. We deployed oyster settlement tiles at 21 intertidal sites throughout Moreton Bay, Australia; a region where > 96% of rock oyster reefs are lost and demand for restoration is high. We quantified effects of variables describing the spatial (from GIS), local habitat (using quadrats and water quality measures), and oyster predator (using underwater videography) characteristics of sites on oyster density and size on tiles. Oyster density was highest at sites with intermediate predator abundance and temperature, highest nearby invertebrate cover, and low and high values of turbidity and nearby rock and algae cover. Conversely, oyster size was highest at sites with intermediate predator density, higher fish species richness and turbidity, and lowest temperatures. Together, this showed that optimal restoration requires sites with 22 to 23 °C average water temperatures, between 10 and 15 oyster predators, and either low (< 2 NTU) or high (> 6 NTU) turbidity levels. Notably, we observed multiple peaks for several variables, suggesting the potential presence of multiple cryptic oyster species on settlement tiles. We found that oysters shared preferred environmental conditions with polychaetes, coralline algae, and tunicates, and were more prevalent and abundant at sites with lower turf algae, barnacle, and mussel cover. Identifying environmental variables influencing oyster population distribution, settlement, and growth can guide the selection and approach of oyster restoration sites.

A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector

Epigenetic patterns including DNA methylation are known to vary between distantly related species, but it is not clear how these patterns differ at an intraspecific level. The sweetpotato whitefly, Bemisia tabaci (Gennadius) (Aleyrodidae; Hemiptera), encompasses several cryptic species. These cryptic species possess highly similar genomes but exhibit substantial biological and physiological differences. B. tabaci cryptic species are invasive, highly polyphagous, and transmit an array of plant infecting single stranded DNA viruses (ssDNA) –begomoviruses. In this study, DNA methylation patterns around genes and genomic features of two prominent B. tabaci cryptic species were investigated following acquisition of a monopartite ssDNA virus –tomato yellow curl virus. The cryptic species investigated included: B (also known as Middle East Asia Minor 1) and Q (also known as Mediterranean). Genomic features, such as promoters, gene bodies, and transposable elements were assessed for methylation levels in both B and Q cryptic species. Despite overall similar trends, both cryptic species showed differences in methylation levels between these genomic features. Virus induced differentially methylated regions were associated with predominantly distinct genes in B and Q cryptic species. All differentially methylated regions were assessed for differential gene expression and alternative splicing events with and without virus acquisition. DNA methylation levels were found to have a negative correlation with differential gene expression in both B and Q cryptic species. The differentially expressed genes were further grouped into hyper- and hypomethylated clusters. These clusters included genes with implications for virus-vector interactions including immune functions and xenobiotics’ detoxification. The observed DNA methylation pattern differences within each cryptic species could, in part, explain some of the biological and physiological differences between them.

From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae)

In this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily’s ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.

The biodiversity of fish in transboundary rivers from north-eastern Bangladesh

The biodiversity of freshwater fish is disappearing at an alarming rate around the globe, with transboundary rivers in Bangladesh being especially vulnerable. From October to December 2023, we surveyed the fish biodiversity of 11 transboundary rivers in north-eastern Bangladesh using the available literature and online FishBase data for species identification. We also added a small number of specimens from our previously examined samples that comprised of 74 fish species belonging to eight orders and twenty-four families. Our survey results indicate that the order Cypriniformes had the biggest number of species (38%), followed by the orders Siluriformes (30%), Perciformes (24%), Clupeiformes (3%), Synbranchiformes (1%), Beloniformes (1%), and Tetraodontiformes (1%). Less than 30% of the entire studied area had 26 fish, indicating that the fish population was confined to a relatively limited region. The total number of species was lower than that we had anticipated, which explains the declining trend of the fish biodiversity in the transboundary rivers of north-eastern Bangladesh. Our survey data have allowed us to gain some early understanding of the hidden biodiversity of fish in these rivers, which may prove useful to other researchers conducting follow-up studies. Since there is currently no published description of the ichthyofaunal diversity in transboundary rivers, the current data on 74 species of ichthyofauna will be useful to future researchers, planners, and policymakers. In order to safeguard the faunal composition of a riverine ecosystem, more efforts incorporating genetic data will be helpful in detecting the biodiversity of fish as well as the cryptic species of other transboundary riverine systems. These efforts will also reinforce the need to re-evaluate the checklist and promote sustainable conservation directions.

Determination of Species Identity and Genetic Diversity of Aedes aegypti and Other Medically Important Mosquitoes of India Using DNA Barcoding.

Aedes aegypti-borne viruses (i.e., dengue, chikungunya, and Zika) have become endemic to India, posing a severe threat to public health. Vector control remains the mainstay of disease management due to nonavailability of licensed vaccines/therapeutics. Conventional morpho-taxonomical methods cannot differentiate between closely related sibling species or species complexes, and hence we evaluated two molecular markers, mitochondrial cytochrome c oxidase subunit 1 (Cox1) and nuclear DNA internal transcribed spacer 2 (-2) gene sequences, to characterize seven populations of Ae. aegypti and four medically important mosquito species (Aedes albopictus, Anopheles stephensi, Culex tritaeniorhyncus, and Culex murrelli). DNA extracted from the 11 mosquito populations (two mosquitoes per population) was polymerase chain reaction amplified, sequenced, and analyzed. Molecular characterization was found to be congruent with morphological identification, suggesting no variants or cryptic species exist in Ae. aegypti and the other mosquitoes studied. Phylogenetic analysis with sequences obtained with Cox1 gene of Ae. aegypti and other Aedes and non-Aedes mosquito species showed clustering of sequences from different species representing different clades, distinctly separating one taxon from the other, whereas ITS-2 sequences of Aedes aegypti from across the world clustered tightly. Nucleotide divergence values revealed a low percentage of intraspecies variation and a higher percentage of interspecies variation. The present study authenticates the applicability of Cox1 and ITS-2 in the precise identification of Ae. aegypti mosquitoes against cryptic or sibling species. Cox1 appeared to be a more reliable marker because it showed distinct clustering of mosquito species, and some sequence variations to represent genetic diversity.

Cryptic genera, cryptic species: phylogeny of the genus Philopteroides Mey, 2004, sensu lato, with descriptions of two new genera and one new species

Closely related chewing lice in the Philopterus-complex are typically morphologically homogeneous, with the most significant differences often being in the male genitalia. However, in many groups within this complex the male genitalia are reduced and lacking one or more element, with the remaining components often at least partially fused. This is not least the case in the genus Philopteroides Mey, 2004, in which the male mesosome is often reduced and other characters are largely homogeneous throughout the genus. A phylogeny of the group based on a combination of mitochondrial and nuclear genes suggests that the species presently placed in Philopteroides belong to three different clades, which do not form a monophyletic group together. We here redefine Philopteroides morphologically, and describe two of these clades as new genera: Stasiasticopterusn. gen. for the species on bulbuls, and Coronedaxn. gen. for species on monarch flycatchers. These genera can be separated from each other and from Philopteroides only by some characters of the male genitalia, but possibly also by characters of the preantennal head and female genitalia. In addition, we describe a new species of Coronedax, Coronedax longicepssp. n. and provide an overview of the morphology of the male genitalia in the three genera treated.

Method development: Assigning sex to African clawless otter spraints and assessing stability of faecal androgen and progestagen metabolites post-defaecation

Monitoring reproductive physiology in wildlife can be a useful tool for assessing population dynamics for conservation and management purposes. Utilizing non-invasive approaches for this, such as quantifying reproductive hormone metabolites from faeces, can be challenging when defaecation events are not observed, or when cryptic species like African clawless otters (Aonyx capensis) are involved. Additionally, test systems for quantifying hormone metabolites in a species for the first time must first be reliably validated prior to use. Our results indicate that Epiandrosterone and Progesterone EIAs are most suitable for determining fAM and fPM concentrations in African clawless otter spraints. The fAM:fPM ratio and respective thresholds are more reliable in sex identification compared to the separate use of individual hormone classes. Sex-related hormone metabolite concentrations remained comparable for up to 12hrs post-defaecation in both sexes.•We screened two androgen and two progestagen enzyme-immunoassays (EIAs) for suitability and reliable quantification of faecal androgen metabolites (fAM) and faecal progestagen metabolites (fPM) in African clawless otters.•We assessed whether the ratio of fAM:fPM concentrations can be used to assign sex to faecal samples from unknown individuals.•We tested the stability of fAM and fPM concentrations post-defaecation to determine the effects of environmental exposure and bacterial metabolism.

Morphological and molecular characterization of cryptic and invasive thrips species in Central India

Morphological and molecular characterization of cryptic and invasive thrips species in Central India

One Genome, Multiple Phenotypes: Would Rhodnius milesi Carcavallo, Rocha, Galvão &amp; Jurberg, 2001 (Hemiptera, Triatominae) Be a Valid Species or a Phenotypic Polymorphism of R. neglectus Lent, 1954?

Species of the Rhodnius genus have a complex taxonomy because the events of phenotypic plasticity and cryptic speciation make it difficult to correctly classify these vectors. During the taxonomic history of the genus, five synonymization events occurred. Additionally, some authors suggest that R. milesi possibly represent only phenotypic polymorphisms of R. neglectus. Thus, we analyzed the specific status of R. milesi in relation to R. neglectus using phylogenetic studies with the mitochondrial gene cytochrome B and the study of reproductive barriers. The phylogenetic reconstruction grouped R. milesi together with R. neglectus from different localities, demonstrating that these taxa represent the same species based on the phylogenetic species concept. Experimental crosses demonstrate the absence of pre- and postzygotic barriers under laboratory conditions. Additionally, when the hatch rates of crosses are compared to intraspecific crosses, it can be noted that they are high and very similar. Finally, the mortality rate of the hybrids does not indicate hybrid inviability, the absence of chromosome pairing errors does not indicate hybrid sterility, and the proportion between male and female hybrids demonstrates that Haldane’s rule was not acting. Therefore, we perform the formal synonymization of R. milesi with R. neglectus.

The Fast Evolution of the Stenobothrini Grasshoppers (Orthoptera, Acrididae, and Gomphocerinae) Revealed by an Analysis of the Control Region of mtDNA, with an Emphasis on the Stenobothrus eurasius Group.

The two cryptic grasshopper species of the genus Stenobothrus, S. eurasius and S. hyalosuperficies, demonstrate different acoustic behavior despite a strong similarity in morphology. A hybridization between these species is possible in the contact zone; however, there are little molecular data about the relationships of these species. The analysis of the mtDNA control region (CR) reveals that haplotypes of S. hyalosuperficies have more in common with the more distant Stenobothrus species than with the closely related S. eurasius. In the contact zone, S. eurasius has mt-haplotypes shared with S. hyalosuperficies, which might indicate an introgression of mtDNA from S. hyalosuperficies to the S. eurasius gene pool. We also analyze the structure and evolutionary rate of the mtDNA CR for the Stenobothrus genus and estimate the time of divergence of the species within the genus. The phylogenetic tree of the tribe Stenobothrini reconstructed with either the CR or COI gave the same four groups. The phylogenetic tree of the Stenobothrus genus has a star-like topology with each mtDNA haplotype found in any analyzed species, except S. eurasius, which forms a separate branch. The maximum degree of incomplete lineage sorting can demonstrate either ancestral polymorphism or introgression.

Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts.

While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbA ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth-Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.