Gerardo Pérez-Ponce de León

What We Don't Recognize Can Hurt Us: A Plea for Awareness About Cryptic Species

Abstract We conducted an extensive literature review on studies that have used DNA sequences to detect cryptic species of parasites during the last decade. Each literature citation that included the term “cryptic” or “sibling” species was analyzed to determine the approach used by the author(s). Reports were carefully filtered to retain only those that recognized the existence of cryptic species centered on the use of DNA sequences. Based on analysis of these papers, we comment on the different ways that parasite cryptic species are discovered in studies focusing on different aspects of the host–parasite relationship, or disciplines, within parasitology. We found a lack of methodological and theoretical uniformity in the discipline for finding and delimiting cryptic species, and we draw attention to the need for standardizing these approaches. We suggest that cryptic species, in the strict sense, are always provisionally cryptic, in that the possibility does exist that new morphological studies or techniques will reveal previously unknown diagnostic structural differences which will permit rapid and practical morphological diagnosis. To avoid future taxonomic confusion, we recommend that parasitologists describe (and formally name) cryptic species following standard taxonomic practice.

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology

Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences.

Abstract. Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.

Parasite inventories and DNA-based taxonomy: lessons from helminths of freshwater fishes in a megadiverse country.

Abstract Freshwater fish helminth parasites are undoubtedly the most well-known group among vertebrate parasites in Mexico; these parasites include 37 adult and 43 larval (metacercariae) species of trematodes, 62 monogeneans, 15 adult and 18 larval (metacestode) cestodes, 6 adult and 4 larval (cystacanth) acanthocephalans, and 54 adult and 15 larval nematodes (L3). Here, we evaluate the extent of the freshwater fish helminth inventory of Mexico using species accumulation curves and discuss the implications of DNA-based taxonomic methods in our understanding of the helminth biodiversity in freshwater fishes. Future directions for the study of the helminth parasites of freshwater fishes are proposed, particularly the role of DNA-based species delimitation criteria in recognizing parasite species, but also in discovering cryptic species. Species accumulation curves indicate that even though the asymptote has not been reached, a tendency toward stabilization is observed in all taxonomic groups except monogeneans. We suggest, therefore, that the inventory, as conventionally understood, is nearing completion for most groups. We suggest that future survey work aimed at enhancing the biodiversity inventory should be strategic, i.e., it should combine the need to target missing components of the host spectrum with the choice of appropriate drainages based on biogeographic, faunistic, and hydrologic data. We also posit that the future belongs to DNA-based taxonomic approaches that aim to uncover previously unrecognized biodiversity.

Detecting a complex of cryptic species within Neoechinorhynchus golvani (Acanthocephala: Neoechinorhynchidae) inferred from ITSs and LSU rDNA gene sequences.

Abstract Neoechinorhynchus golvani is an intestinal parasite of freshwater and brackish water fishes distributed in Mexico. The genetic variability of 40 samples representing 12 populations from north, south, and central Mexico, and 1 from Costa Rica, was estimated by sequencing 2 nuclear genes (ITS1, 5.8S, ITS2, and LSU rDNA, including the domain D2 + D3). The length of both genes ranged from 700 to 779 base pairs (bp) and from 813 to 821 bp, for ITSs and LSU, respectively. The genetic divergence among populations ranged from 19.5 to 35.3% with ITSs and from 9.28 to 19.58% with LSU. Maximum likelihood and maximum parsimony analyses were performed for each data set and also for 2 combined data sets (ITSs + LSU rDNA with and without outgroups), showing strong similarities among trees, with high bootstrap support in all cases. Genetic divergence, in combination with phylogenetic analyses, suggested that the acanthocephalan N. golvani represents a complex of cryptic species, which is composed of at least 3 lineages. The first lineage, corresponding with N. golvani, shows a wide distribution, including localities from northeastern Mexico, southwards through central and southeastern Mexico, and further down to Costa Rica. This lineage is associated with cichlid fishes in strictly freshwater environments. Lineages 2 and 3 are distributed in brackish water systems along the Gulf of Mexico and Pacific slopes, respectively; both are associated with eleotrid fishes, and apparently represent 2 cryptic species. The diversification of the eleotrid and cichlid lineages seems to be the result of independent host-switching events from the ancestral population.

Differentiation of Mexican Species of Haematoloechus Looss, 1899 (Digenea: Plagiorchiformes): Molecular and Morphological Evidence

Molecular evidence is interpreted in the light of morphology to examine the validity of several species of Haematoloechus described as Mexican endemics. Internal transcribed spacers 1 and 2 and 28S ribosomal genes were sequenced for 11 isolates. Phylogenetic analysis of separate partitions and combined databases was conducted. Results were analyzed, in the light of morphological evidence. Haematoloechus macrorchis is proposed as a junior synonym of Haematoloechus longiplexus. Haematoloechus pulcher is a sibling species with Haematoloechus complexus in Lerma wetlands. In Mexico, Haematoloechus medioplexus is distributed along the east coast coinciding with the distribution of Rana berlandieri. The sister species of H. medioplexus is Haematoloechus coloradensis, sharing the distribution of the uterus as a synapomorphic character. Haematoloechus illimis is more closely related to H. medioplexus and H. coloradensis than to H. complexus. It can be distinguished by the distribution of the uterus, lobed ovary, and testes.

Phylogenetic analysis of nuclear and mitochondrial DNA reveals a complex of cryptic species in Crassicutis cichlasomae (Digenea: Apocreadiidae), a parasite of Middle-American cichlids.

We obtained nuclear ITS-1 and mitochondrial cox1 sequences from 225 Crassicutis cichlasomae adults collected in 12 species of cichlids from 32 localities to prospect for the presence of cryptic species. This trematode is commonly found in species of cichlids over a wide geographic range in Middle-America. Population-level phylogenetic analyses of ITS-1 and cox1, assessments of genetic and haplotype diversity, and morphological observations revealed that C. cichlasomae represents a complex of seven cryptic species for which no morphological diagnostic characters have been discovered thus far. Bayesian and Maximum Likelihood analyses of concatenated datasets (906 bp) recovered eight lineages of C. cichlasomae, all with high posterior probabilities and bootstrap branch support. Values of genetic divergence between clades ranged from 1.0% to 5.2% for ITS-1, and from 7.2% to 30.0% for cox1. Morphological study of more than 300 individuals did not reveal structural diagnostic traits for the species defined using molecular evidence. These observations indicate that some traditional morphological characters (e.g., testes position) have substantial intra-specific variation, and should be used with caution when classifying C. cichlasomae and their sister taxa. Additionally, phylogenetic analyses did not reveal a strict correlation between these cryptic species and their host species or geographic distribution, however it appears that genetic distinctiveness of these cryptic species was influenced by the diversification and biogeographical history of Middle-American cichlids.

Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class polyacanthocephala (acanthocephala)

Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. These results are consistent with the view of Polyacanthocephala representing an independent class within Acanthocephala.

Adult Endohelminth Parasites of Ictalurid Fishes (Osteichthyes: Ictaluridae) in Mexico: Empirical Evidence for Biogeographical Patterns

Abstract The helminth fauna of Mexican ictalurids was investigated through original surveys and published literature in order to evaluate the biogeography of host-parasite associations of a primarily nearctic host group in a major faunal transition area. In total, 84 specimens of 4 species of ictalurids (Ictalurus balsanus, Ictalurus dugesi, Ictalurus furcatus, and Ictalurus punctatus) were sampled from 7 localities in 5 hydrological drainages. Ten species of adult endohelminths were recovered from this survey, including 4 species of digeneans (Phyllodistomum lacustri, Genarchella tropica, Alloglossidium corti, and Campechetrema sp.), 3 cestodes (Corallobothrium fimbriatum, Megathylacoides giganteum, and Choanoscolex lamothei), and 3 nematodes (Dichelyne mexicanus, Goezia sp., and Rhabdochona sp.). The adult helminth fauna of ictalurids reported in this study is composed of taxa that are typical of ictalurids in other parts of North America, north of Mexico. This core fauna (in a historical biogeographic sense) includes the corallobothriines C. fimbriatum and M. giganteum and the digeneans P. lacustri and A. corti. Two other helminths, C. lamothei and D. mexicanus, may be added to this group in the future. Other helminths occurred sporadically and provide evidence for host-sharing (ecological host extensions), but we were unable to identify any valid cases of host-switching from more distantly related hosts. The helminth fauna provides evidence that the ictalurids developed their characteristic helminth fauna without neotropical influences and that the phylogenetic affinities of the ictalurids do not appear to be with any neotropical siluriform.

STATUS OF CORYNOSOMA (ACANTHOCEPHALA: POLYMORPHIDAE) BASED ON ANATOMICAL, ECOLOGICAL, AND PHYLOGENETIC EVIDENCE, WITH THE ERECTION OF PSEUDOCORYNOSOMA N. GEN

The possession of genital spines has been considered as a key taxonomic trait to differentiate Corynosoma from other genera of the Polymorphidae. However, Corynosoma currently consists of 2 groups of species with clear ecological and morphological divergences: the “marine” group (with ca. 30 species) infects mammals and piscivorous birds in the marine realm, whereas the “freshwater” group (with ca. 7 species) infects waterfowl in continental waters. Species from these groups differ in shape of body and neck, trunk spination, lemnisci length and shape, testes arrangement, and number and shape of cement glands. We tested whether species from these 2 groups formed a monophyletic assemblage based on a phylogenetic analysis by using 15 morphological characters. We also included species of Andracantha, Polymorphus, and Hexaglandula with which potential taxonomic conflicts could most likely arise. We obtained 108 equally most parsimonious trees of 32 steps, with a consistency index (CI) = 0.59, and a retention index (RI) = 0.82. The strict consensus tree indicated that the “freshwater” species of Corynosoma form a monophyletic assemblage closely related to some species of Polymorphus, whereas the “marine” species of Corynosoma are grouped together with Andracantha. Accordingly, Corynosoma is not a monophyletic assemblage, and Pseudocorynosoma n. gen. is proposed for the “freshwater” species of Corynosoma. This decision was strongly supported by (1) a functional comparison of foretrunk muscles between species of Polymophus, Andracantha, and Corynosoma; (2) a multivariate morphometric study of proboscis characters and egg size; and (3) an analysis of ecological patterns of host–parasite relationships.