Discordant molecular and morphological evolution in buffalofishes (Actinopterygii: Catostomidae)

Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus)

Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing ('genome skimming'). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species' native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data. These sites were used to classify Ictiobus spp. samples with genome-skim data, along with a larger set (n = 67) where ultraconserved elements (UCEs) were sequenced. Analyses of whole mitochondrial data revealed more limited signal. Nearly all samples matched their purported species based on morphologic identification, but two Missouri samples morphologically identified as I. niger grouped with samples of I. bubalus, albeit with significant enrichment of I. niger SNPs. To our knowledge this is the first report of a DNA-based tool to reliably discriminate these three morphologically distinct species.

Haff disease associated with consumption of buffalofish (Ictiobus spp.) in the United States, 2010-2020, with confirmation of the causative species

BACKGROUND

In the United States, buffalofish (Ictiobus spp.) are sporadically associated with sudden onset muscle pain and weakness due to rhabdomyolysis within 24 h of fish consumption (Haff disease). Previous genetic analyses of case-associated samples were unable to distinguish the three species of buffalofish that occur in the US, Ictiobus cyprinellus (bigmouth buffalo), Ictiobus bubalus (smallmouth buffalo), and Ictiobus niger (black buffalo).

METHODS

Ten events were investigated between 2010 and 2020 and demographic and clinical information was collected for 24 individuals. Meal remnants were collected from 5 of 10 events with additional associated samples (n = 24) collected from another five of 10 events. Low-coverage whole-genome sequencing (genome skimming) was used to identify meal remnants.

RESULTS

Patients (26-75 years of age) ranged from 1-4 per event, with 90% involving ≥2 individuals. Reported symptoms included muscle tenderness and weakness, nausea/vomiting, and brown/tea-colored urine. Median incubation period was 8 h. Ninety-six percent of cases were hospitalized with a median duration of four days. The most commonly reported laboratory finding was elevated creatine phosphokinase and liver transaminases. Treatment was supportive including intravenous fluids to prevent renal failure. Events occurred in California (1), Illinois (2), Louisiana (1), New York (1), Mississippi (1), Missouri (2), New Jersey (1), and Texas (1) with location of harvest, when known, being Illinois, Louisiana, Mississippi, Missouri, Texas, and Wisconsin. Meal remnants were identified as I. bubalus (n = 4) and I. niger (n = 1). Associated samples were identified as I. bubalus (n = 16), I. cyprinellus (n = 5), and I. niger (n = 3).

DISCUSSION

Time course, presentation of illness, and clinical findings were all consistent with previous domestic cases of buffalofish-associated Haff disease. In contrast to previous reports that I. cyprinellus is the causative species in US cases, data indicate that all three buffalofish species are harvested but I. bubalus is most often associated with illness.

Ichthyological Differentiation and Homogenization in the Pánuco Basin, Mexico

Species introductions and extirpations are key aspects of aquatic ecosystem change that need to be examined at large geographic and temporal scales. The Pánuco Basin (Eastern Mexico) has high ichthyological diversity and ecological heterogeneity. However, freshwater fish (FWF) introductions and extirpations since the mid-1900s have modified species range and distribution. We examine changes in FWF species composition in and among four sub-basins of the Pánuco by comparing fish collection records pre-1980 to 2018. Currently, the FWF of the Pánuco includes 95 species. Fishes in the Poeciliidae, Cyprinidae, and Cichlidae, respectively, comprised most records over time. Significant differences in species composition were found between the first (pre-1980) and last (2011–2018) study periods, but not for periods in-between. Eight independent species groups were key for explaining changes in Pánuco river ichthyofauna; one group was dominated by invasive species, and saw increases in the number of records across study periods (faunal homogenization). Another group was formed by species with conservation concern with a declining number of records over time. Thirteen (2 native and 11 non-native) species were responsible for temporal turnover. These results strongly suggest high rates of differentiation over time (via native species loss) following widespread non-native species introductions.

Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data

The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.

Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals

The original distribution area of the Patagonian 'pejerrey' Odontesthes hatcheri has been subjected to the introduction of a related species; the Bonaerensean 'pejerrey' Odontesthes bonariensis. This species currently coexists with O. hatcheri in lakes and reservoirs, and can interbreed and produce fertile hybrid offspring. The purposes of this study were; a) the extensive sampling of Patagonian and Andean-Cuyan populations of pejerrey, b) the species identification according to taxonomic key, c) validation of taxonomic results on the basis of mitochondrial DNA composition, and d) applying morphometric analysis to explore the effects of hybridization and environmental conditions on body shape. Cytochrome b sequence analysis showed a high degree of genetic divergence between species and low intraspecific variation in O. hatcheri. Geometric Morphometric Analyses detected shape differences in agreement with diagnostic characteristics of each species. Putative hybrids exhibiting intermediate diagnostic characteristics were identified by Geometric Morphometric Analysis. Significant regressions between body shape and total phosphorus and altitude were found, suggesting a dependence on trophic web structure. This multi-level approach suggests the introgression of O. bonariensis into several O. hatcheri populations throughout Patagonia. Managers should take this into account when considering further exotic introductions into regions where non-native fishes have not yet become established.

Phylogeny of suckermouth catfishes (Mochokidae: Chiloglanis) from Kenya: the utility of Growth Hormone introns in species level phylogenies

African suckermouth catfishes (Mochokidae: Chiloglanis) occur in freshwater throughout tropical Africa. Specimens from all major drainages across Kenya were collected over three field seasons. Here we present a phylogeny inferred from both mitochondrial cytochrome b (cyt b) and introns of the nuclear Growth Hormone gene (GH). The phylogeny inferred from introns is largely congruent with the results from an analysis of cyt b. The length and variability of GH introns make them ideal species level nuclear markers without the problem of introgression commonly encountered with mitochondrial genes. This analysis confirmed the presence of two previously known undescribed Chiloglanis species and also suggests the presence of previously unknown diversity within the Athi River system. The resulting phylogeny also indicates the presence of two separate lineages within C. brevibarbis. The historical biogeography of Chiloglanis within Kenya is discussed. The utility of GH intron for species level phylogenies of Siluriformes is compared to that in other groups.

An approach to identify putative hybrids in the 'coalescent stochasticity zone', as exemplified in the African plant genus Streptocarpus (Gesneriaceae)

The inference of phylogenetic relationships is often complicated by differing evolutionary histories of independently-inherited markers. The causes of the resulting gene tree incongruence can be challenging to identify, often relying on coalescent simulations dependent on unverifiable assumptions. We investigated alternative techniques using the South African rosulate species of Streptocarpus as a study group. Two independent gene trees - from the nuclear ITS region and from three concatenated plastid regions (trnL-F, rpl20-rps12 and trnC-D) - displayed widespread, strongly supported incongruence. We investigated the causes by detecting genetic exchange across morphological borders using morphological optimizations and genetic exchange across species boundaries using the genealogical sorting index. Incongruence between gene trees was associated with ancestral shifts in growth form (in four species) but not in pollination syndrome, suggesting introgression limited by reproductive barriers. Genealogical sorting index calculations showed polyphyly of two additional species, while individuals of all others were significantly associated. In one case the association was stronger according to the internal transcribed spacer data than according to the plastid data, which, given the smaller effective population size of the plastid, may also indicate introgression. These approaches offer alternative ways to identify potential hybridization events where incomplete lineage sorting cannot be rejected using simulations.

Phylogenetic relationships and biogeography of Pseudoxiphophorus (Teleostei: Poeciliidae) based on mitochondrial and nuclear genes

Phylogenetic relationships of species of genus Pseudoxiphophorus have been only tackled in detail based on morphology so far. However, phylogenetic evidence based on molecular data is still lacking. In this study, we have used five molecular markers (mitochondrial cytb, 16S, atp6-8, and nuclear actB and S7) to reconstruct a robust, inclusive phylogeny of Pseudoxiphophorus. Our phylogenetic results strongly disagree with the main morphological hypothesis, and indicate different phylogenetic relationships among the recognized species of Pseudoxiphophorus. Pseudoxiphophorus jonesii is recovered as the sister group of all other Pseudoxiphophorus lineages, and this initial splitting may be associated to the extension of the Mexican Neovolcanic Plateau at the Punta del Morro site (event used to calibrate our dating analysis). The branch leading to all other Pseudoxiphophorus separated subsequently into two major groups, one comprising those lineages occurring in southern Mexico and Guatemala-Belize, and another with those lineages that extended further southwards to Honduras and Nicaragua. This event took place during the Pliocene, and is likely associated with periods of inundation of the Polochic-Motagua fault area. The Isthmus of Tehuantepec also appears to have been a strong biogeographic barrier triggering cladogenesis in Pseudoxiphophorus. Heterandria formosa (traditionally placed as sister to Pseudoxiphophorus) is not sharing the most recent common ancestor with Pseudoxiphophorus, and is recovered as more distantly related to them. Furthermore, Pseudoxiphophorus bimaculatus (the most cosmopolitan species) is also recovered as a polyphyletic assemblage that appears to comprise those Pseudoxiphophorus that have not been assigned to the other eight, more localized species. All this suggests that Pseudoxiphophorus needs a major taxonomic revision as a whole in order to incorporate all existing diversity.

Complex evolutionary history of the Mexican stoneroller Campostoma ornatum Girard, 1856 (Actinopterygii: Cyprinidae)

Background

Studies of the phylogeography of Mexican species are steadily revealing genetic patterns shared by different species, which will help to unravel the complex biogeographic history of the region. Campostoma ornatum is a freshwater fish endemic to montane and semiarid regions in northwest Mexico and southern Arizona. Its wide range of distribution and the previously observed morphological differentiation between populations in different watersheds make this species a useful model to investigate the biogeographic role of the Sierra Madre Occidental and to disentangle the actions of Pliocene tecto-volcanic processes vs Quaternary climatic change. Our phylogeographic study was based on DNA sequences from one mitochondrial gene (cytb, 1110 bp, n = 285) and two nuclear gene regions (S7 and RAG1, 1822 bp in total, n = 56 and 43, respectively) obtained from 18 to 29 localities, in addition to a morphological survey covering the entire distribution area. Such a dataset allowed us to assess whether any of the populations/lineages sampled deserve to be categorised as an evolutionarily significant unit.

Results

We found two morphologically and genetically well-differentiated groups within C. ornatum. One is located in the northern river drainages (Yaqui, Mayo, Fuerte, Sonora, Casas Grandes, Santa Clara and Conchos) and another one is found in the southern drainages (Nazas, Aguanaval and Piaxtla). The split between these two lineages took place about 3.9 Mya (CI = 2.1-5.9). Within the northern lineage, there was strong and significant inter-basin genetic differentiation and also several secondary dispersal episodes whit gene homogenization between drainages. Interestingly, three divergent mitochondrial lineages were found in sympatry in two northern localities from the Yaqui river basin.

Conclusions

Our results indicate that there was isolation between the northern and southern phylogroups since the Pliocene, which was related to the formation of the ancient Nazas River paleosystem, where the southern group originated. Within groups, a complex reticulate biogeographic history for C. ornatum populations emerges, following the taxon pulse theory and mainly related with Pliocene tecto-volcanic processes. In the northern group, several events of vicariance promoted by river or drainage isolation episodes were found, but within both groups, the phylogeographic patterns suggest the occurrence of several events of river capture and fauna interchange. The Yaqui River supports the most diverse populations of C. ornatum, with several events of dispersal and isolation within the basin. Based on our genetic results, we defined three ESUs within C. ornatum as a first attempt to promote the conservation of the evolutionary processes determining the genetic diversity of this species. They will likely be revealed as a valuable tool for freshwater conservation policies in northwest Mexico, where many environmental problems concerning the use of water have rapidly arisen in recent decades.