Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece

Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation

Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree-building efforts, yet the impacts of backbone tree completeness and species composition remain under-explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by "placing" COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA-ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%-78% missing species are correctly placed (by EPA-ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA-ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood-based EPA-ng consistently provide higher accurate placements than the distance-based APPLES. In conclusion, COI-based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.

Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.

The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons

Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.

Barcoding Fails to Delimit Species in Mongolian Oedipodinae (Orthoptera, Acrididae)

Mongolia, a country in central Asia, with its vast grassland areas represents a hotspot for Orthoptera diversity, especially for the Acrididae. For Mongolia, 128 Acrididae species have been documented so far, of which 41 belong to the subfamily Oedipodinae (band-winged grasshoppers). Yet, few studies concerning the distribution and diversity of Oedipodinae have been conducted in this country. Molecular genetic data is almost completely absent, despite its value for species identification and discovery. Even, the simplest and most used data, DNA barcodes, so far have not been generated for the local fauna. Therefore, we generated the first DNA barcode data for Mongolian band-winged grasshoppers and investigated the resolution of this marker for species delimitation. We were able to assemble 105 DNA barcode (COI) sequences of 35 Oedipodinae species from Mongolia and adjacent countries. Based on this data, we reconstructed maximum likelihood and Bayesian inference phylogenies. We, furthermore, conducted automatic barcode gap discovery and used the Poisson tree process (PTP) for species delimitation. Some resolution was achieved at the tribe and genus level, but all delimitation methods failed to differentiate species by using the COI region. This lack of resolution may have multiple possible reasons, which likely differ between taxa: the lack of resolution in the Bryodemini may be partially explained by their massive genomes, implying the potential presence of large numbers of pseudogenes, while within the Sphingonotini incomplete lineage sorting and incorrect taxonomy are more likely explanations for the lack of signal. Further studies based on a larger number of gene fragments, including nuclear DNA, are needed to distinguish the species also at the molecular level.

Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty

The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.

Population genomics of helminth parasites

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Monogeneans and chubs: Ancient host-parasite system under the looking glass

Host-parasite coevolution is one of the fundamentals of evolutionary biology. Due to the intertwined evolutionary history of two interacting species and reciprocal coadaptation processes of hosts and parasites, we can expect that studying parasites will shed more light onto the evolutionary processes of their hosts. Monogenea (ectoparasitic Platyhelminthes) and their cyprinoid fish hosts represent one of the best models for studying host-parasite evolutionary relationships using a cophylogenetic approach. These parasites have developed remarkably high host specificity, where each host species often serves as a potential host for its own host-specific monogenean species. Here, the cophylogenetic relationships in the Dactylogyrus-Squalius system was investigated, as Squalius is one of several cyprinoid genera with puzzling phylogeography and inhabits all four major peri-Mediterranean peninsulas. Of 29 endemic Squalius species examined for the presence of Dactylogyrus parasites, a total of 13 Dactylogyrus species were collected from the gills of 20 Squalius species across a wide range of distribution. Phylogenetic reconstruction revealed a polyphyletic origin for Dactylogyrus species parasitizing congeneric Squalius, with four major clades being recognized. On the basis of the delimitation of host specificity, strict specialists parasitizing single host species, geographic specialists parasitizing congeners in a limited geographical region, and true generalists parasitizing congeners in various geographical regions were recognized in Dactylogyrus species parasitizing Squalius. The phylogenetic reconstruction of Squalius hosts revealed two major clades, the first encompassing only peri-Mediterranean species and the second including species from other Euro-Asian regions. Distance-based cophylogenetic methods did not reveal a statistically significant global cophylogenetic structure in the studied system; however, several host-parasite links among Iberian endemic species contributed significantly to the overall structure. The widest host range and associated genetic variability were recorded for D. folkmanovae, parasitizing nine Squalius species, and D. vistulae, parasitizing 13 Squalius species. Two different dispersion mechanisms and morphological adaptations to Squalius hosts were clearly reflected in the contrasting cophylogenetic patterns for these two species with different levels of host specificity. While host-parasite cospeciation plays an important role in diversification within D. folkmanovae, diversification within D. vistulae is driven mainly by host switching.

Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation

Background

The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids.

Results

We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48].

Conclusions

These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02085-8.

Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula

The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.

Multi-locus genetic analyses of Quasipaa from throughout its distribution

Montane frogs of the genus Quasipaa Dubois, 1992 occur from southern China to Southeast Asia (Frost 2021). Analyses of mtDNA (Cytb) and nuDNA data (Rag1, Rag2, Rhod, Tyr) for samples from 93 localities throughout its distribution yield a phylogeny. Clades A and B occur in Southeast Asia, clade C in northern Yangtze River, China, clade D in southwestern China, and clades E and F in southeastern China. Results place Q. yei within monophyletic Quasipaa and identify two new species. Based on nuDNA data, the basal split of clade A and B indicates an Indochinese origin of Quasipaa. The west-east diversification of five species across South China (Q. spinosa, Q. exilispinosa, Q. jiulongensis, Q. shini, Q. boulengeri) corresponds to topographic terrains II and III of China. Divergence of species from southeastern China (Q. shini, Q. jiulongensis, Q. spinosa, Q. exilispinosa) and southwestern China (Q. boulengeri) dates to 15.30-16.56 Ma (million years ago). A principal component analysis (PCA) and t-test involving 19 bioclimatic variables identifies significantly different environmental conditions between the two regions. Species' distribution models (SDM) for Q. spinosa and Q. boulengeri identify the best areas to be eastern and western South China, respectively. Thus, environmental variation appears to have influenced the genetic divergence and distributions of Quasipaa in South China. Mito-nuclear discordance indicates that some individuals of Q. exilispinosa and Q. spinosa hybridized historically.

Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea

To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.

Uncovering the diversity of monogeneans (Platyhelminthes) on endemic cypriniform fishes of the Balkan Peninsula: new species of Dactylogyrus and comments on their phylogeny and host-parasite associations in a biogeographic context

Seven new species of Dactylogyrus Diesing, 1850 (Dactylogyridae) are described from the gills of seven endemic species of cyprinoids (Cyprinidae, Leuciscidae) inhabiting the Balkan Peninsula: Dactylogyrus romuli n. sp. from Luciobarbus albanicus (Greece), Dactylogyrus remi n. sp. from Luciobarbus graecus (Greece), Dactylogyrus recisus n. sp. from Pachychilon macedonicum (Greece), Dactylogyrus octopus n. sp. from Tropidophoxinellus spartiaticus (Greece), Dactylogyrus vukicae n. sp. from Delminichthys adspersus (Bosnia and Herzegovina), Dactylogyrus leptus n. sp. from Chondrostoma knerii (Bosnia and Herzegovina), and Dactylogyrus sandai n. sp. from Telestes karsticus (Croatia). To delineate species boundaries, we used an integrative taxonomic approach combining morphological and genetic data. With these tools, we illustrate that some species of monogeneans considered as cryptic might be designated as pseudocryptic (morphologically similar, not easily differentiated) after a posteriori detailed morphological examination, as happened with D. romuli n. sp. and D. remi n. sp. Thus, for accurate species characterization, it is particularly important to acquire both morphological and molecular data from the same individual specimens, ideally along with illustrations of taxonomically important structures directly taken from hologenophores. Using phylogenetic reconstruction, we investigated the phylogenetic position of newly described Dactylogyrus species within Dactylogyrus species from Balkan cyprinoids with regard to morphological characteristics, host range, and geographical distribution.

Testing mate recognition through reciprocal crosses of two native populations of the whitefly Bemisia tabaci (Gennadius) in Australia

Bemisia tabaci (Gennadius) represents a relatively large cryptic species complex. Australia has at least two native populations of B. tabaci sensu lato and these were first found on different host plants in different parts of Australia. The species status of these populations has not been resolved, although their mitochondrial sequences differ by 3.82-4.20%. We addressed the question of whether these AUSI and AUSII B. tabaci populations are distinct species. We used reciprocal cross-mating tests to establish whether the insects from these different populations recognize one another as potential mating partners. The results show that the two native Australian populations of B. tabaci have a mating sequence with four phases, each of which is described. Not all pairs in the control crosses mated and the frequency of mating differed across them. Some pairs in the AUSI-M × AUSII-F did mate (15%) and did produce female progeny, but the frequency was extremely low relative to controls. Microsatellite genotyping of the female progeny produced in the crosses showed these matings were successful. None of the AUSII-M × AUSI-F crosses mated although some of the males did search for females. These results demonstrate the critical role of the mate recognition process and the need to assess this directly in cross-mating tests if the species status of different populations is to be tested realistically. In short, AUSI and AUSII B. tabaci populations are distinct species because the individual males and females do not recognize individuals of the alternative population as potential mating partners.

Limited long-distance dispersal success in a Western European fairy shrimp evidenced by nuclear and mitochondrial lineage structuring

Anostraca are known by their ability for long-distance dispersal, but the existence in several species of deep, geographically structured mtDNA lineages suggests their populations are subjected to allopatric differentiation, isolation, and prevalence of local scale dispersion. Tanymastix stagnalis is one of the most widespread species of Anostraca and previous studies revealed an unclear geographical pattern of mtDNA genetic diversity. Here, we analyze populations from the Iberian and Italian Peninsulas, Central Europe, and Scandinavia, with the aim to characterize the patterns of genetic diversity in a spatio-temporal framework using mtDNA and nuclear markers to test gene flow among close populations. For these aims we built a time-calibrated phylogeny and carried out Bayesian phylogeographic analyses using a continuous diffusion model. Our results indicated that T. stagnalis presents a deeply structured genetic diversity, including 7 ancient lineages, some of them even predating the Pleistocene. The Iberian Peninsula harbors high diversity of lineages, with strong isolation and recent absence of gene flow between populations. Dispersal at local scale seems to be the prevailing dispersal mode of T. stagnalis, which exhibits a pattern of isolation-by-distance in the Iberian Peninsula. We remark the vulnerability of most of these lineages, given the limited known geographic distribution of some of them, and the high risk of losing important evolutionary potential for the species.

High diversity of fish ectoparasitic monogeneans (Dactylogyrus) in the Iberian Peninsula: a case of adaptive radiation?

The epicontinental fauna of the Iberian Peninsula is strongly influenced by its geographical history. As the possibilities for dispersion of organisms into and from this region were (and still are) limited, the local fauna consists almost exclusively of endemic species. Almost all Iberian freshwater fishes of the families Leuciscidae and Cyprinidae are endemic and on-going research on these taxa continually uncovers new species. Nevertheless, information on their host-specific parasites remains scarce. In this study, we investigate the diversity and phylogenetic relationships in monogeneans of the genus Dactylogyrus (gill ectoparasites specific to cyprinoid fish) in the Iberian Peninsula. Twenty-two species were collected and identified from 19 host species belonging to Cyprinidae and Leuciscidae. A high degree of endemism was observed, with 21 Dactylogyrus species reported from Iberia only and a single species, D. borealis, also reported from other European regions. Phylogenetic analysis split the endemic Iberian Dactylogyrus into two well-supported clades, the first encompassing Dactylogyrus parasitizing endemic Luciobarbus spp. only, and the second including all Dactylogyrus species of endemic leuciscids and four species of endemic cyprinids. Species delimitation analysis suggests a remarkable diversity and existence of a multitude of cryptic Dactylogyrus species parasitizing endemic leuciscids (Squalius spp. and representatives of Chondrostoma s.l.). These results suggest a rapid adaptive radiation of Dactylogyrus in this geographically isolated region, closely associated with their cyprinoid hosts. Moreover, phylogenetic analysis supports that Dactylogyrus parasites colonized the Iberian Peninsula through multiple dispersion events.

Multilocus phylogenetic analysis helps to untangle the taxonomic puzzle of chubs (genus Squalius: Cypriniformes: Actinopteri) in the Adriatic basin of Croatia and Bosnia and Herzegovina

Fish of the genus Squalius inhabit various freshwater habitats across Europe and Asia, with a particularly high diversity in the Mediterranean area, but the taxonomic status of many populations is still a matter of debate. This study aims to resolve the taxonomic uncertainties of chubs distributed in the Adriatic basin of Croatia and Bosnia and Herzegovina. Phylogenetic reconstruction based on the mitochondrial gene for cytochrome b and two nuclear genes, the recombination activating gene 1 and the rhodopsin gene, reveal high diversity of chubs in the investigated area. Two evolutionary independent groups are revealed: the first comprising the species Squalius illyricus, S. microlepis, S. svallize, S. tenellus and S. zrmanjae, and a second group corresponding with S. squalus. Genetic distinctiveness of species belonging to different groups is high due to their divergence that began in the Middle Miocene. In addition to allopatric speciation as the main force of divergence of Adriatic Squalius species, several instances of natural hybridizations were detected, contributing to the observed diversity. A comparison of phylogenetic scenarios using Bayesian factors corroborated the molecular basis for recognition of six Squalius species in the Adriatic basin, while Squalius janae is confirmed to be a junior synonym of S. squalus.

Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers

The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome-wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans-Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter-riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression

Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.

Bidirectional mitochondrial introgression between Korean cobitid fish mediated by hybridogenetic hybrids

Genomic introgression through interspecific hybridization has been observed in some species of the freshwater fish family Cobitidae. Within this family, a Cobitis hankugensis-Iksookimia longicorpa diploid-triploid hybrid species complex on the Korean peninsula is unique in displaying hybridogenesis, a unisexual reproduction mode that allows hybrids to mediate the transfer of mitochondrial DNA (but not nuclear DNA) between the two parent species. However, populations of the parental species in the wild have never been examined for the potential effect of introgression on their genomes. To address the genetic consequences of unisexual hybridization on the parental species, we examined genetic structure of the two parental species, C. hankugensis and I. longicorpa, in three independent natural habitats where they coexist with their hybrid complex using DNA sequence data of one mitochondrial gene and three nuclear genes. We found that mitochondrial introgression between the two species was extensive in all the examined localities, while there was no evidence of nuclear introgression across the species boundary. This result indicates that the hybridogenetic individuals mediate mitochondrial introgression from one species to the other, producing mito-nuclear mosaic genomes such as C. hankugensis nuclear genomes associated with I. longicorpa mitochondrial DNA and the reverse. The direction and degree of introgression varied among the three localities, but the underlying mechanisms for this observation proved elusive. Introgression might depend on which species serves as the predominant sperm or ovum donor or the environmental conditions of the localities. The present study suggests that introgressive hybridization between pure C. hankugensis and I. longicorpa species is highly likely where the two species co-occur with hybridogenetic individuals, but the consequence of introgression could be variable due to the history and environmental characteristics of particular populations across the parental species' ranges.

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.

Phylogeography of the widespread creek chub Semotilus atromaculatus (Cypriniformes: Leuciscidae)

The extent and nature of genetic differentiation in Semotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear intron s7 gene for S. atromaculatus and all other congeners as well as representative species from all other genera in the creek chub-plagopterin clade. The phylogeography of major haplogroups of S. atromaculatus was also assessed according to variation in a fragment of the mitochondrial cytb region from 567 individuals across its range. All analyses identified S. thoreauianus, S. lumbee and S. corporalis as reciprocally monophyletic groups. Analyses of nuclear sequence variation resolved S. atromaculatus as a single clade, where S. thoreauianus and S. lumbee were recovered as the sister group to S. atromaculatus, and S. corporalis was resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recovered S. atromaculatus as three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group to S. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito-nuclear discordance and phylogeographic differentiation within S. atromaculatus illustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.

Validity of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes) upheld in phylogenomic analysis

Higher systematics within the Digenea, Carus 1863 have been relatively stable since a phylogenetic analysis of partial nuclear ribosomal markers (rDNA) led to the erection of the Diplostomida Olson, Cribb, Tkach, Bray, and Littlewood, 2003. However, recent mitochondrial (mt) genome phylogenies suggest this order might be paraphyletic. These analyses show members of two diplostomidan superfamilies are more closely related to the Plagiorchiida La Rue, 1957 than to other members of the Diplostomida. A recent phylogeny based on partial cytochrome c oxidase I also indicates one of the groups implicated, the Diplostomoidea Poirier, 1886, is non-monophyletic. To determine if these results were robust to additional taxon sampling, we analyzed mt genomes from seven diplostomoids in three families. To choose between phylogenetic alternatives based on mt genomes and the prior rDNA-based topology, we analyzed hundreds of ultra-conserved genomic elements assembled from shotgun sequencing. The Diplostomida was paraphyletic in the mt genome phylogeny but supported in the ultra-conserved genomic element phylogeny. We speculate this mitonuclear discordance is related to ancient, rapid radiation in the Digenea. Both ultra-conserved genomic elements and mt genomes support the monophyly of the Diplostomoidea and show congruent relationships within it. The Cyathocotylidae Mühling, 1898 are early diverging descendants of a paraphyletic clade of Diplostomidae Poirier, 1886, in which are nested members of the Strigeidae Railliet, 1919; the results support prior suggestions that the Crassiphialinae Sudarikov, 1960 will rise to the family level. Morphological traits of diplostomoid metacercariae appear to be more useful for differentiating clades than those of adults. We describe a new species of Cotylurus Szidat, 1928, resurrect a species of Hysteromorpha Lutz, 1931, and find support for a species of Alaria Schrank, 1788 of contested validity. Complete rDNA operons from seven diplostomoid species are provided as a resource for future studies.

The phylogenetic relationships and species richness of host-specific Dactylogyrus parasites shaped by the biogeography of Balkan cyprinids

Parasites exhibiting a high degree of host specificity are expected to be intimately associated with their hosts. Therefore, the evolution of host-specific parasites is at least partially shaped by the evolutionary history and distribution of such hosts. Gill ectoparasites of Dactylogyrus (Monogenea) are specific to cyprinid fish. In the present study, we investigated the evolutionary history of 47 Dactylogyrus species from the Balkan Peninsula, the Mediteranean region exhibiting the highest cyprinid diversity in Europe, and from central European cyprinids. Phylogenetic analyses revealed four well-supported clades of endemic and non-endemic Dactylogyrus spp. with four basal taxa. Endemic cyprinids with a limited distribution range were parasitized by endemic Dactylogyrus species, but some of them shared several Dactylogyrus species with central European cyprinids. Species delimitation analyses based on molecular data suggest that Dactylogyrus diversity is higher than that defined from morphology. Some endemic cyprinid species harboured Dactylogyrus species of different origins, this probably resulting from multiple host switching. Our results support the view that the evolution of Dactylogyrus in the Balkans has been influenced not only by the historical dispersion and distribution of their cyprinid hosts, but also by recent contacts of non-native cyprinid species with endemic cyprinid fauna in this region.

The first mitochondrial genome of the model echinoid Lytechinus variegatus and insights into Odontophoran phylogenetics

Assembly of publically available next-generation sequence data facilitated the generation of three camarodont echinoid mitogenomes: two for the Green Urchin (Lytechinus variegatus) and one for the Red Urchin (Mesocentrotus franciscanus). The data generated are exploited in a phylogenomic analysis of the superfamily Odontophora, originally proposed for echinoids with tooth supports on the epiphyses of the jaw. The analysis highly supports this taxon and its current subdivision into three families: the Echinometridae, Toxopneustidae, and Strongylocentrotidae. The analysis furthermore implies that historical taxonomic issues between two members of the genus Strongylocentrotus (S. pallidus and S. droebachiensis) may have a genetic basis. The novel mitogenomes for the model species L. variegatus complements the draft genome available for this taxon, one of only three genome-enabled echinoid species. The assembly method applied herein, follows a divide-and-conquer approach that provides for reduced computational requirements and facilitates resolving assembly problems when processing ultra-high coverage next-generation sequence data.