Unexpected but unsurprising lineage diversity within the most widespread Neotropical crocodilian genus Caiman (Crocodylia, Alligatoridae)

Hemogregarine Diversity Infecting Brazilian Turtles with a Description of Six New Species of Haemogregarina (Apicomplexa: Adeleorina: Haemogregarinidae)

(1) Background: Hemoparasites of the genus Haemogregarina (Haemogregarinidae) are commonly reported in freshwater turtles. However, in Brazil, only three species have currently been characterised using molecular methods. This study aimed to bring new insights on the diversity of species of Haemogregarina infecting Brazilian freshwater turtles from Mato Grosso and Goiás states using molecular and morphological tools. (2) Methods: In total, 2 mL of blood was collected, with between two to five blood smears prepared, fixed with absolute methanol, and stained with a 10% Giemsa solution. Blood was stored at −20 °C for molecular analysis targeting the 18S rRNA gene. Fragments of the organs (liver, spleen, heart, and kidney) were separated and stained with hematoxylin-eosin. (3) Results: A total of 40 turtles were screened and hemogregarines were observed in 34 (85%) individuals (3 Podocnemis expansa and 31 Podocnemis unifilis). Haemogregarina embaubali and six new species of Haemogregarina were observed and formally described as follows: H. unifila n. sp., H. rubra n. sp., H. goianensis n. sp., H. araguaiensis n. sp., H. tigrina n. sp., and H. brasiliana n. sp. (4) Conclusions: This study contributes to the diversity and knowledge of Brazilian fresh-water turtle blood parasites, using integrative approaches for diagnosing and characterizing hemoparasites, with the identification of six undescribed species.

Phylogeographical analysis and phylogenetic inference based on the cytochrome b gene in the genus Caiman (Crocodylia: Alligatoridae) in Central and South America

The genus Caiman is one of the most taxonomically conflicted among crocodilians. Caiman crocodilus has four subspecies: Caiman crocodilus crocodilus, Caiman crocodilus fuscus, Caiman crocodilus chiapasius and Caiman crocodilus apaporiensis, but some studies recognize Caiman yacare as a subspecies of C. crocodilus or as a C. crocodilus–C. yacare complex. In Argentina, Caiman latirostris and C. yacare are present and included in sustainable use programmes, although they have hardly been studied at the genetic level. The present study had two main objectives: (1) to study the genetic diversity, structure and phylogeny of C. yacare and C. latirostris in Argentina; and (2) to perform a phylogenetic analysis of the genus Caiman throughout its entire distribution. The results show high haplotype diversity for both species but low nucleotide diversity for C. latirostris. Phylogenetic analysis shows a clear separation between both species but, surprisingly, a well-differentiated clade belonging to the Chaco region was observed. The phylogenetic analysis exhibited clades made up of the sequences of each Caiman species, with some inconsistencies: in the clade of C. crocodilus, one sequence of C. yacare is included, and one clade is observed including sequences from C. c. fuscus and C. c. chiapasius. These data indicate the need to undertake interdisciplinary studies to clarify the taxonomic status of these crocodilian species.

Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.

Update: Assessing the evolutionary trajectory of the Apaporis caiman (Caiman crocodilus apaporiensis, Medem 1955) via mitochondrial molecular markers

The spectacled caiman (Caiman crocodilus) is currently considered to be a species complex due to the relatively high morphological and molecular diversity expressed across its range. One of the populations of interest, inhabiting the Apaporis River (Colombia), was described based on skull features as an incipient species (C. c. apaporiensis) and has been treated by some authors as a full species. Recent molecular work challenged this hypothesis, because relatively low mitochondrial molecular differentiation was found between the morphologically described Apaporis caiman and C. crocodilus (s.s.) Amazonian populations. Here, we present an update on the topic based on a larger molecular sample size and on analysis of expanded geometric morphometric data that include six newly collected skulls. Morphometric data support the existence of previously recognized morphotypes within the complex in Colombia and demonstrate that the newly collected material can be assigned to the classic Apaporis caiman morphotype. However, our expanded genetic analysis fails to find appreciable mitochondrial molecular divergence of the Apaporis caiman population from the C. c. crocodilus population (COI-CytB: Amazon Peru 0.17 ± 0.06%, CytB-only: Caquetá River Colombia 0.08 ± 0.07%). The Apaporis caiman is interpreted to be a phenotypically distinct member of the cis-Andean C. crocodilus metapopulation that has not yet achieved (or may not be undergoing at all) appreciable genetic differentiation. Thus, it should not be considered a fully independent evolutionary lineage, nor given full species rank.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

Fish biodiversity of a tropical estuary under severe anthropic pressure (Doce River, Brazil)

Abstract The Doce River has undergone severe changes over the last centuries (e.g., flow regulation, pollution, habitat and species loss). Here, we present the first comprehensive fish biodiversity assessment of the Doce River estuary and a summary of the main impacts and their drivers for the whole river since the early 18th century. Carangiformes, Siluriformes and Eupercaria incertae sedis were the most representative orders for the 115 species recorded. Most species are native (87.8%), euryhaline/peripheral (80%) and zoobenthivorous (33.9%). Threatened (Paragenidens grandoculis, Genidens barbus, and Lutjanus cyanopterus) and near threatened (Cynoscion acoupa, Dormitator maculatus, Lutjanus jocu, Lutjanus synagris, and Mugil liza) species are peripheral. Thirteen species are exotic at the country (Butis koilomatodon, Coptodon rendalli, and Oreochromis niloticus) or the basin level (e.g., Pygocentrus nattereri and Salminus brasiliensis). The catfish Cathorops cf. arenatus is reported for the first time on the eastern coast of Brazil and Paragenidens grandoculis, considered extinct in the Doce River, was discovered in the estuary.

The contribution of ontogenetic growth trajectories on the divergent evolution of the crocodylian skull table

To explore shape variability among crocodylian skull tables, an analysis using geometric morphometric methods is conducted with the inclusion of extant and fossil taxa. Skull tables are variable and the differences likely play a role in hydrodynamics, species recognition, and biomechanical adaptations. Comparisons of allometric change within taxa are explored revealing that adults significantly diverge from juvenile skull table morphologies in most species and these changes happen in a stereotyped way. In all analyses, adults of the smallest extant taxa plot alongside the juveniles of related taxa and heterochrony may explain the maintenance of these morphologies into adulthood. When landmarks representing the supratemporal fenestrae are included, longirostrine taxa are broadly separated from one another due to variation in the size of the supratemporal fenestrae. The hypotheses of previous studies suggesting that the size of the supratemporal fenestrae is influenced by snout length-with longer snouts corresponding to larger fenestrae-must be re-evaluated. Although species of the crocodyloids Tomistoma and Euthecodon approach or exceed the length of the snout in gavialoids, their supratemporal fenestrae are proportionally smaller-this suggests a phylogenetic constraint in crocodyloids regardless of snout length.

From the river to the ocean: mitochondrial DNA analyses provide evidence of spectacled caimans (Caiman crocodilus Linnaeus 1758) mainland–insular dispersal

There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Phylogeny and systematics of the Proterodiplostomidae Dubois, 1936 (Digenea: Diplostomoidea) reflect the complex evolutionary history of the ancient digenean group

The Proterodiplostomidae Dubois, 1936 is a relatively small family of diplostomoidean digeneans parasitising the intestines of reptilian hosts associated with freshwater environments in tropical and subtropical regions. The greatest diversity of proterodiplostomids is found in crocodilians, although some parasitise snakes and turtles. According to the most recent revision, the Proterodiplostomidae included 17 genera within 5 subfamilies. Despite the complex taxonomic structure of the family, availability of testable morphology-based phylogenetic hypotheses and ancient hosts, molecular phylogenetic analyses of the group were practically lacking. Herein, we use novel DNA sequence data of the nuclear lsrRNA gene and mitochondrial cox1 gene from a broad range of proterodiplostomid taxa obtained from crocodilian, fish, and snake hosts on four continents to test the monophyly of the family and evaluate the present morphology-based classification system of the Proterodiplostomidae in comparison with the molecular phylogeny. This first detailed phylogeny for the Proterodiplostomidae challenges the current systematic framework. Combination of molecular phylogenetic data with examination of freshly collected quality specimens and re-evaluation of morphological criteria resulted in a number of systematic and nomenclatural changes along with a new phylogeny-based classification of the Proterodiplostomidae. As the result of our molecular and morphological analyses: (i) the current subfamily structure of the Proterodiplostomidae is abolished; (ii) three new genera, Paraproterodiplostomum n. g., Neocrocodilicola n. g. and Proteroduboisia n. g., are described and Pseudoneodiplostomoides Yamaguti, 1954 is restored and elevated from subgenus to genus level; (iii) two new species, Paraproterodiplostomum currani n. g., n. sp. and Archaeodiplostomum overstreeti n. sp., are described from the American alligator in Mississippi, USA. Comparison of the structure of terminal ducts of the reproductive system in all proterodiplostomid genera did not support the use of these structures for differentiation among subfamilies (or major clades) within the family, although they proved to be useful for distinguishing among genera and species. Our study includes the first report of proterodiplostomids from Australia and the first evidence of a snake acting as a paratenic host for a proterodiplostomid. A key to proterodiplostomid genera is provided. Questions of proterodiplostomid-host associations parasitic in crocodilians are discussed in connection with their historical biogeography. Our molecular phylogeny of the Proterodiplostomidae closely matches the current molecular phylogeny of crocodilians. Directions for future studies of the Proterodiplostomidae are outlined.