Cryptic Morphology Research Articles

Molecular phylogeny and cryptic morphology: A combined approach to taxonomic novelties in Polycarpaea (Caryophyllaceae) from Vietnam.

Three new species of Polycarpaea from Vietnam, Polycarpaea vanphongensis V.T. Tran, H.T. Truong & N.V. Binh, Polycarpaea chungana V.T. Tran, H.T. Truong & N.V. Binh, Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh are described and illustrated based on evidence of molecular sequence data from two markers (ITS1-5.8S-ITS2 and rps16) and combined morphological characteristics. Polycarpaea vanphongensis is closely related to Polycarpaea gaudichaudi Gagnep., Polycarpaea arenaria (Lour.) Gagnep., Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh but differs by its stem glabrous, leaf ovate to elliptic, glabrous, ovary oblong ovoid, base obtuse, apex attenuate, capsule oblong void, 3.8 mm long. Polycarpaea phuquocensis V.T. Tran, H.T. Truong & N.V. Binh differs from the three species mentioned above by its stem being densely villous, leaf spathulate, ciliate, ovary ovoid, base acute, apex obtuse, capsule ovoid, 1.2 mm long. Polycarpaea chungana V.T. Tran, H.T. Truong & N.V. Binh is most similar to Polycarpaea lignosa Gagnep., but differs in having leaf oblong or linear, sparse ciliate, sepal and petal apex deeply concaved or slightly bifid, ovary ovoid, ovoid, 0.8-1.0 mm long. Furthermore, the achievements of analysis using molecular data on the systematic positions of 7 other species are results that have not been in previous molecular analyses.

Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant

Host specificity is a key factor influencing the ecology and evolutionary diversification of parasitic organisms. Host specialisation and geographic isolation are known to lead to the genetic differentiation of allopatric races in parasitic plants. However, how divergence can co-occur in sympatry remains largely unknown. We investigated phenological and phenotypic differentiation and potential reproductive isolation among three sympatric genetic races of Cytinus hypocistis (Cytinaceae) - an extreme endophytic holoparasite with a high degree of host specialisation. We compared spatio-temporal variations in flowering phenology, flower production, floral longevity, floral rewards, and morphology, and conducted inter-race pollinations among three races parasitising Cistus ladanifer, C. salviifolius, and Halimium halimifolium (Cistaceae) in six co-occurring populations. We found that host-defined genetic races differed significantly across multiple phenotypic and phenological aspects – a phenomenon previously overlooked due to the plants’ cryptic morphology. The race parasitising H. halimifolium showed earlier blooming, higher floral display, longer flowers, and higher pollen production and nectar concentration; the race on C. salviifolius showed later flowering, significantly lower floral display and smaller flowers with lower floral rewards; the race on C. ladanifer had intermediate characteristics. Genetic races were interfertile yet may remain differentiated by restricted gene flow and host-driven selection pressures. Together, our data point to a rare case of sympatric divergent evolution hiding in plain sight: apparently morphologically similar co-occurring parasite races can be genetically, phenotypically, and phenologically distinct. This hitherto unreported example of host-driven sympatric diversification challenges how species concepts are applied to cryptic parasitic plant races.

New species of the elusive crickets from the genus Pendleburyella Chopard, 1969 (Gryllidae, Pentacentrinae) from Sabah, Borneo.

Only one species of Pendleburyella Chopard, 1969 (Gryllidae, Pentacentrinae) was previously known to occur in Borneo: Pendleburyella eirmosa Tan, Muhammad & Wahab, 2023 from Brunei Darussalam. Here, two additional new species of crickets from the genus Pendleburyella are described from the highlands of Sabah, Borneo: Pendleburyella eremita sp. nov. from Bukit Hampuan and Pendleburyella nimba sp. nov. from Mount Trus Madi. In total, six species of Pendleburyella are currently known, three from Borneo and three from Malay Peninsula. It is likely that many more species are awaiting discovery owing to its cryptic morphology and elusive nature.

A phylogenetic and taxonomic assessment of the Cnemaspis alwisi group (Reptilia: Gekkonidae) in Sri Lanka with a description of two new species from isolated misty-mountains

Sri Lanka is a local hotspot for Cnemaspis day geckos with 40 currently known species with 100% endemism. In this paper, we evaluate the phylogenetic relationships of Cnemaspis species belonging to the alwisi group of the podihuna clade and describe two additional new species of Cnemaspis from Sri Lanka; one from Galgiriya mountain, Kurunegala District, and another from Ethagala mountain, Ampara District. These new species were recorded from granite caves within forested areas in isolated mountains in the dry bioclimatic zone (point-endemics). Both new species are microhabitat specialists with narrow niches limited to humid, cool, canopy-shaded granite caves and old buildings associated with granite caves, where they are camouflaged by their cryptic morphology and body colouration. Furthermore, both species prefer narrow (~ 6–12 mm), long (~ 120–450 mm) and deep (~ 80–260 mm) crevices as refugia. The regions in which these habitats are located receive relatively low annual rainfall (1,000–1,500 mm). These new species are medium in size (28.5–36.8 mmSVL) and can be differentiated from all other Sri Lankan Cnemaspis by the presence of clearly enlarged, subhexagonal subcaudal scales and the absence of precloacal pores in males. Both species described here are categorised herein as Critically Endangered (CR) under the IUCN Red List criteria. The major threats for these new species are habitat loss due to expansion of commercial-scale agriculture, illicit forest encroachments, and forest fires. Therefore, we recommend that relevant authorities take immediate conservation action to ensure the protection of these forest areas with their buffer zones in the near future.

Integrative taxonomy reveals that not all European reddish runcinids are the same: the case of the Runcina ferruginea Kress, 1977 (Gastropoda, Heterobranchia, Runcinida) species-complex, with the description of a new genus

Owing to the small size and cryptic morphology, runcinids are among the most difficult marine heterobranchs to study and consequently one of the groups about which little is known. Only recently were molecular tools and phylogenetics first employed to study the systematics. The charismatic European reddish-brown species Runcina ferruginea Kress, 1977, first described from Plymouth, UK, is a paradigm of the challenges facing the taxonomy of these slugs. Due to similarities between R. ferruginea and the Croatian species R. zavodniki described by Thompson, 1980, the latter has been considered as a junior synonym. However, molecular phylogenetics revealed the occurrence of a complex of four species masked under the name R. ferruginea. Through an integrative approach, combining multi-locus (COI, 16S rRNA and histone H3) molecular phylogenetics and morpho-anatomical characters (shape and colouration of body, radula, gizzard plates and reproductive systems) based on specimens from south-western UK, and the central and western Mediterranean Sea (Spain, France, Italy and Croatia), we redescribe R. ferruginea proper and confirm R. zavodniki as a valid species. Also, two new species are described, one belonging to the genus Runcina (R. lupiaensis sp. nov.) and the other to the new genus Pseudoruncina gen. nov. (Pseudoruncina marinae gen. et sp. nov.). Our study exposes the occurrence of cryptic diversity among runcinids and stresses the need for additional work to understand the diversity of this group of minute molluscs. ZooBank: urn:lsid:zoobank.org:pub:2611EF7D-7762-40CE-BD04-B6D9AB70F2AA.

Germling culture and molecular analysis of evasive micro-filamentous green algae growing in the Maltese islands (central Mediterranean)

Abstract Various species of marine micro-filamentous green algae (<5 mm) remain overlooked globally. They are difficult to identify in field collections due to their diminutive size and their cryptic morphology. During this study, algal cultures combined with DNA barcoding helped to overcome these challenges. Both substratum samples and macrophytic fragments of Posidonia oceanica, Dictyopteris sp. and Halopteris sp. were incubated in laboratory culture. Germlings of Ulvella endostraca and Blastophysa rhizopus grew from the incubated substratum. Blastophysa rhizopus is a new record for the Maltese islands, as is U. endostraca that had only been reported previously from New Zealand. In situ, germlings of both species were also observed to grow as epiphytes, on Dictyopteris sp. in the case of U. endostraca, and on P. oceanica in the case of B. rhizopus. This study employed the in vitro culture of algal germlings, as well as morphological and molecular analyses. DNA data and subsequent phylogenetic analyses of tufA and rbcL sequences supported the separation of U. endostraca from other closely related congeners that have been previously reported from the Maltese islands. Moreover, this study includes a comparison of the micro-filamentous algae identified from Malta with those from other areas of the Mediterranean Sea.

Identifying cryptic fern gametophytes using DNA barcoding: A review.

Ferns and lycophytes are unique among land plants in having sporophyte (diploid) and gametophyte (haploid) generations that can grow independently of each other. While most studies of fern ecology focus on the more visible sporophytic stage, the gametophyte is critically important, as it is the sexual phase of the life cycle. Yet, fern gametophytes have long been neglected in field studies due to their small size and cryptic morphology. DNA barcoding is a powerful method that can be used to identify field‐collected gametophytes to species and allow for detailed study of their ecology. Here, we review the state of DNA barcoding as applied to fern gametophytes. First, we trace the history of DNA barcoding and how it has come to be applied to fern gametophytes. Next, we summarize case studies that show how DNA barcoding has been used to better understand fern species distributions, gametophyte ecology, and community ecology. Finally, we propose avenues for future research using this powerful tool, including next‐generation DNA sequencing for in‐field identification of cryptic gametophytes.

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance.

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation‐related actions.

Electronic identification keys for species with cryptic morphological characters: a feasibility study using some Thesium species

The popularity of electronic identification keys for species identification has increased with the rapid technological advancements of the 21st century. Although electronic identification keys have several advantages over conventional textual identification keys and work well for charismatic species with large and clear morphological characters, they appear to be less feasible and less effective for species with cryptic morphology (i.e. small, obscure, variable characters and/or complicated structures associated with terminology that is difficult to interpret). This is largely due to the difficulty in presenting and illustrating cryptic morphological characters unambiguously. When taking into account that enigmatic species with cryptic morphology are often taxonomically problematic and therefore likely exacerbate the taxonomic impediment, it is clear that species groups with cryptic morphology (and all the disciplines dependent on their correct identification) could greatly benefit from a user-friendly identification tool, which clearly illustrates cryptic characters. To this end, the aim of this study was to investigate and develop best practices for the unambiguous presentation of cryptic morphological characters using a pilot interactive photographic identification key for the taxonomically difficult plant genus Thesium (Santalaceae), as well as to determine its feasibility. The project consisted of three stages: (1) software platform selection, (2) key construction and (3) key evaluation. The proposed identification key was produced with Xper3 software and can be accessed at http://www.xper3.fr/xper3GeneratedFiles/publish/identification/1330098581747548637/mkey.html. Methodologies relating to amongst others, character selection and delineation, visual and textual descriptions, key construction, character coding and key evaluation are discussed in detail. Seventeen best practices identified during this study are subsequently suggested for future electronic key compilation of species with cryptic morphology. This study indicates that electronic identification keys can be feasible and effective aids for the identification of species with cryptic morphological characters when the suggested best practices are followed.

Phylogeographic analysis reveals mito-nuclear discordance in Dasypterus intermedius

Abstract Northern yellow bats (Dasypterus intermedius) are tree-roosting bats in the family Vespertilionidae comprised of two subspecies: D. intermedius intermedius and D. intermedius floridanus. The two subspecies are thought to be geographically separated. Due to their cryptic morphology, this hypothesis has never been tested and can benefit from being examined within a molecular framework. In this study, mitochondrial sequence data from 38 D. intermedius and nuclear sequence data from 14 D. intermedius from across their range were used to test the hypothesis that genetically defined groups correspond geographically with the two morphologically defined subspecies. Although high levels of divergence of the mitochondrial sequence (11.6%) suggest genetically distinct clusters sympatric in southern Texas, no genetic structure was recovered with the nuclear marker. Moreover, the mitochondrial sequence data recovered a paraphyletic relationship between the two subspecies of D. intermedius with the Cuban yellow bat (D. insularis), whereas no such paraphyly was recovered from analysis of the nuclear marker. Divergence time based on analyses of mitochondrial sequence for the two subspecies was approximately 5.5 Ma. The patterns observed are hypothesized to be the result of past isolation of lineages and secondary contact that is currently contributing to gene flow.

Determining levels of cryptic diversity within the endemic frog genera, Indirana and Walkerana, of the Western Ghats, India.

A large number of species in the tropics are awaiting discovery, many due to their cryptic morphology ie. lack of discernable morphological difference. We explored the presence of cryptic lineages within the frog genera, Indirana and Walkerana, which are endemic to the Western Ghats of Peninsular India. By reconstructing a phylogeny using 5 genes and robust geographic sampling, we delimited 19 lineages along a population—species continuum, using multiple criteria including haplotype clusters, genetic distance, morphological distinctness, and geographical separation. Of these 19 lineages, 14 belonged to the genus Indirana and 5 to the genus Walkerana. Divergence dating analyses revealed that the clade comprising Indirana and Walkerana began diversifying around 71 mya and the most recent common ancestor of Indirana and Walkerana split around 43 mya. We tested for the presence of cryptic lineages by examining the relationship between genetic and morphological divergence among related pairs within a pool of 15 lineages. The pairs showed strong morphological conservatism across varying levels of genetic divergence. Our results highlight the prevalence of morphologically cryptic lineages in these ancient endemic clades of the Western Ghats. This emphasizes the significance of other axes, such as geography, in species delimitation. With increasing threats to amphibian habitats, it is imperative that cryptic lineages are identified so that appropriate conservation measures can be implemented.

Lingering Taxonomic Challenges Hinder Conservation and Management of Global Bonefishes

Despite expanding research on the popular recreational fishery, bonefish taxonomy remains murky. The genus Albula, comprising these iconic circumtropical marine sportfishes, has a complex taxonomic history driven by highly conserved morphology. Presently, 12 putative species are spread among 3 species complexes. The cryptic morphology hinders visual identification, requiring genetic species identification in some cases. Unclear nomenclature can have unintended consequences, including exacerbating taxonomic uncertainty and complicating resolution efforts. Further, ignoring this reality in publications may erode management and conservation efforts. In the Indian and Pacific oceans, ranges and areas of overlap are unclear, precluding certainty about which species support the fishery and hindering conservation efforts. Species overlap, at both broad and localized spatial scales, may mask population declines if one is targeted primarily (as demonstrated in the western Atlantic fishery). Additional work is necessary, especially to increase our understanding of spatiotemporal ecology across life history stages and taxa. If combined with increased capacity to discern between cryptic species, population structure may be ascertained, and fisheries stakeholders will be enabled to make informed decisions. To assist in such efforts, we have constructed new range maps for each species and species complex. For bonefishes, conservation genomic approaches may resolve lingering taxonomic uncertainties, supporting effective conservation and management efforts. These methods apply broadly to taxonomic groups with cryptic diversity, aiding species delimitation and taxonomic revisions.

Integrative taxonomy of the rock-dwelling gecko Cnemaspis siamensis complex (Squamata, Gekkonidae) reveals a new species from Nakhon Si Thammarat Province, southern Thailand.

The rock-dwelling gecko genus Cnemaspis is one of the most species-diverse genera of gekkonid in Thailand. Earlier studies relied on morphological data to identify species, but cryptic morphology often obscured species diversity in Cnemaspis. In this study, an integrative taxonomic approach based on morphological characters and sequences of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene were used to clarify current taxonomy of the Cnemaspis siamensis complex and delimit a new species from Lan Saka District, Nakhon Si Thammarat Province, southern Thailand. Cnemaspis lineatubercularissp. nov. is distinguished from other congeneric species by the combination of morphological characters: (1) maximum snout-vent length (SVL) of 40.6 mm (mean 38.8 ± SD 1.4, N = 12) in adult males and maximum SVL of 41.8 mm (mean 39.5 ± SD 1.9, N = 7) in adult females; (2) 8–9 supralabial and infralabial scales; (3) gular, pectoral, abdominal, and subcaudal scales keeled; (4) rostral, interorbitals, supercilium, palmar scales, and ventral scales of brachia smooth; (5) 5–6 small, subconical spine-like tubercles present on flanks; (6) 19–21 paravertebral tubercles linearly arranged; (7) 27–29 subdigital lamellae under the fourth toe; (8) 4–7 pore-bearing precloacal scales, pores rounded arranged in chevron shape and separated only in males; (9) one postcloacal tubercles each side in males; (10) ventrolateral caudal tubercles present anteriorly; (11) caudal tubercles restricted to a single paravertebral row on each side; (12) single median row of subcaudal scales keeled and lacking enlarged median row; and (13) gular region, abdomen, limbs and subcaudal region yellowish only in males. Genetically, the uncorrected pairwise divergences between the new species and their congeners in the C. siamensis group were between 15.53–28.09%. The new species is currently known only from granitic rocky streams at Wang Mai Pak Waterfall in the Nakhon Si Thammarat mountain range. Its discovery suggests that additional unrecognized species of Cnemaspis may still occur in unexplored areas of southern Thailand.

Multimammate mice of the genus Mastomys (Rodentia: Muridae) in Ethiopia – diversity and distribution assessed by genetic approaches and environmental niche modelling

Multimammate mice of the genus Mastomys are widespread in sub-Saharan Africa and occur in a wide range of open habitats. Representatives of this genus are the most common African rodents, the main vertebrate agricultural pests and vectors of human pathogens. In Ethiopia, the biogeographically most complex eastern African country, several species have been reported, but their distribution has never been described because of their cryptic morphology. Here we present genetically identified species from 377 Ethiopian Mastomys specimens and analyse their distributional patterns. The genus, represented by four species, inhabits most of the country, with the exception of the highest mountains and dry areas, such as the Afar triangle and the Somali region. For the first time we document M. kollmannspergeri from a single locality in the northernmost part of Ethiopia. Three previously recorded species are more widespread – M. erythroleucus was found at 32 localities, M. natalensis at 13 localities and the Ethiopian endemic species M. awashensis at 18 localities. Phylogenetic analysis of mitochondrial cytochrome b gene sequences indicates that only one of the six phylogroups of M. natalensis and one of the four phylogroups of M. erythroleucus are represented in Ethiopia. Haplotype network analysis indicates two subclades of Ethiopian M. erythroleucus separated by the Ethiopian Rift Valley. Using presence records, we constructed distribution models for the species and analysed the level of overlap. The predicted distribution shows most overlap between M. awashensis and M. natalensis, which is in agreement with empirical data as both species were found in sympatry at four localities. A medium level of overlap was predicted between M. natalensis and M. erythroleucus and both species were found co-existing at two localities. This study not only presents the first detailed distribution of cryptic Mastomys species, but also clearly identifies multimammate mice as model taxa for future evolutionary studies (e.g. the evolution of coexistence or host-parasite interactions) and indicates the regions suitable for such studies.

Strong Population Structure and Differentiation within and among Burrowing Bog Crayfish Species of Southern Alabama Wetlands

Despite their high diversity and degree of endemism in the southeastern US, little is known about population genetic structure of most crayfishes. This is because of their cryptic morphology and elusive behavior, particularly burrowing species. We compared population genetic structure of 2 burrowing crayfish species (Creaserinus burrisi and C. byersi) from bogs in Washington, Baldwin, and Mobile counties in southern Alabama, USA. Through hand excavation of burrows, we collected individuals from 7 drainage systems, with C. byersi in the southern extent and C. burrisi in the northern extent of the study area. Based on mitochondrial cytochrome oxidase subunit I (COI) gene sequences, tests of pairwise genetic structure approached the upper limit of 1.0, showed that haplotype sharing between and within drainages was nearly non-existent. Large differentiation between and low genetic diversity both between and within drainage systems occurred for both species. Genetic structuring corresponded to subtle hydrologic features such as fine-scale drainage patterns and human development (road crossings). Our data suggest that these species have recently diverged with extremely low vagility and rare dispersal events, resulting in isolated populations. Such population uniqueness from a genetic perspective pose considerable challenges to range-wide management of these and other similar species.

DNA barcodes expose unexpected diversity in Canadian mites.

Mites (Arachnida: Acariformes, Parasitiformes) are the most abundant and species-rich group of arthropods in soil, but are also diverse in freshwater habitats, on plants, and as symbionts of larger animals. However, assessment of their diversity has been impeded by their small size and often cryptic morphology. As a consequence, published estimates of their species richness span more than two orders of magnitude (0.4-114million). In this study we employ DNA barcoding and the Barcode Index Number (BIN) system to investigate mite diversity at over 1,800 sites across Canada, primarily from soil and litter habitats with smaller contributions from freshwater, plants, and animal hosts. Barcodes from 73,394 specimens revealed 7,077 BINs with representatives from all four orders (Ixodida, Mesostigmata, Sarcoptiformes, Trombidiformes) and 60% (186) of the known families. The BIN total is 2.4 times the number of species previously recorded from Canada (2,999), reflecting the unexpectedly high richness of several families. Richness projections suggest that more than 28,000 BINs occur at the sampled locations, indicating that the Canadian mite fauna almost certainly includes more than 30,000 species-a total similar to that for the most diverse insect order in Canada, Diptera. This unexpected diversity was partitioned into highly dissimilar, spatially-structured assemblages that likely reflect dispersal limitation and environmental heterogeneity. Further sampling of a greater diversity of habitats will refine understanding of mite diversity in Canada, but similar analyses in other geographic regions will be essential to ascertain their diversity at a global scale.

Investigating the Clitellata (Annelida) of Icelandic springs with alternative barcodes

DNA barcoding is an invaluable tool to identify clitellates, regardless of life stage or cryptic morphology. However, as COI (the standard barcode for animals) is relatively long (658 bp), sequencing it requires DNA of high quality. When DNA is fragmented due to degradation, alternative barcodes of shorter length present an option to obtain genetic material. We attempted to sequence 187 clitellates sampled from springs in Iceland. However, the material had been stored at room temperature for two years, and DNA of the worms had degraded, and only three COI sequences were produced (i.e., <2% success rate). Using two alternative barcodes of 16S (one ca. 320 bp, the other ca. 70 bp long) we increased the number of sequenced specimens to 51. Comparisons of the 16S sequences showed that even the short 70 bp fragment contained enough genetic variation to separate all clitellate species in the material. Combined with morphological examinations we recognized a total of 23 species, where at least 8 are new records for Iceland, some belonging to genera new for Iceland: Cernosvitoviella and Pristina. All the new taxa are included in an updated species list of Icelandic Clitellata. The material revealed some stygophilic species previously known to inhabit springs, but true stygobionts, which are restricted to groundwater habitats, were not found. Our study shows that short 16S fragments can be obtained from DNA too degraded to be used in traditional COI barcoding, and contain enough genetic variation to separate closely related clitellate species.

Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat

Tilletia species cause diseases on grass hosts with some causing bunt diseases on wheat (Triticum). Two of the four species infecting wheat have restricted distributions globally and are subject to quarantine regulations to prevent their spread to new areas. Tilletia indica causes Karnal bunt and is regulated by many countries while the non-regulated T. walkeri is morphologically similar and very closely related phylogenetically, but infects ryegrass (Lolium) and not wheat. Tilletia controversa causes dwarf bunt of wheat (DB) and is also regulated by some countries, while the closely related but non-regulated species, T. caries and T. laevis, both cause common bunt of wheat (CB). Historically, diagnostic methods have relied on cryptic morphology to differentiate these species in subsamples from grain shipments. Of the DNA-based methods published so far, most have focused on sequence variation among tested strains at a single gene locus. To facilitate the development of additional molecular assays for diagnostics, we generated whole genome data for multiple strains of the two regulated wheat pathogens and their closest relatives. Depending on the species, the genomes were assembled into 907 to 4633 scaffolds ranging from 24 Mb to 30 Mb with 7842 to 9952 gene models predicted. Phylogenomic analyses confirmed the placement of Tilletia in the Exobasidiomycetes and showed that T. indica and T. walkeri were in one clade whereas T. controversa, T. caries and T. laevis grouped in a separate clade. Single copy and species-specific genes were identified by orthologous group analysis. Unique species-specific genes were identified and evaluated as suitable markers to differentiate the quarantine and non-quarantine species. After further analyses and manual inspection, primers and probes for the optimum candidate genes were designed and tested in silico, for validation in future wet-lab studies.

Morphological and molecular analysis of cryptic native and invasive freshwater snails in Chile

Species delimitation in minute freshwater snails is often difficult to perform using solely shell morphology. The problem intensifies when invasive species spread within the distribution range of morphologically similar native species. In Chile, the Truncatelloidean snails are represented by the native genera Heleobia and Potamolithus plus the invasive mudsnail Potamopyrgus antipodarum, which can easily be confused. Using an integrative approach, we performed molecular phylogenetic analysis and studied reproductive and morphological features to identify superficially similar forms inhabiting the central area of the country. Truncatelloidean snails were identified in 40 of 51 localities sampled, 10 containing Potamopyrgus antipodarum, 23 Heleobia and 7 Potamolithus. Based on these results and previously published data, the known distribution of the mudsnail in Chile encompasses 6 hydrological basins, including 18 freshwater ecosystems. The finding of the mudsnails in several type localities of native species/subspecies of “Heleobia” that were not find in situ suggests species replacement or significant extinction of native fauna, a hypothesis supported by the restudy of type material that shows that endemic forms belong to the genus Potamolithus. This study shows the usefulness of integrative taxonomy not only resolving complex taxa with cryptic morphology but also measuring the extent of an ongoing invasion.

Unveiling the cryptic morphology and ontogeny of the Colombian Caiman crocodilus: a geometric morphometric approach

Caiman crocodilus is an alligatoroid broadly distributed in the neotropics from Mexico to Brazil, where Colombia is the only country that has the complete subspecies complex distributed in its territory. This species has been the focus of many genetic, ecological and morphological studies. However, these studies are limited to traditional morphology methods or have limitations to examine interspecific variation among the four subspecies reported in Colombia. This is the first study of intraspecific variation in the skull of Caiman crocodilus complex distributed in Colombia, using a two-dimensional approach of geometric morphometric on 122 post-hatching ontogenetic cranial series. Morphological differences between species and changes during ontogeny (snout increases its length and, skull roof and orbits decrease their proportions) that represents part of morphological changes in the cranial ontogeny of crocodilians were found. In the morphospace, there was a significant differentiation of C. crocodilus apaporiensis and C. crocodilus crocodilus from C. crocodilus fuscus and C. crocodilus chiapasius. Results from this study revealed that C. crocodilus apaporiensis is a differentiated group from the global complex as well as that the specimens of C. crocodilus chiapasius collected from Medem in Colombia may be showing cryptic morphology in some traits.