Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)

The advent of genomic methods allows us to revisit the evolutionary history of organismal groups for which robust phylogenies are still lacking, particularly in species complexes that frequently hybridize. In this study, we conduct RAD-sequencing (RAD-seq) analyses of midwife toads (genus Alytes), an iconic group of western Mediterranean amphibians famous for their parental care behavior, but equally infamous for the difficulties to reconstruct their evolutionary history. Through admixture and phylogenetic analyses of thousands of loci, we provide the most comprehensive phylogeographic framework for the A. obstetricans complex to date, as well as the first fully resolved phylogeny for the entire genus. As part of this effort, we carefully explore the influence of different sampling schemes and data filtering thresholds on tree reconstruction, showing that several, slightly different, yet robust topologies may be retrieved with small datasets obtained by stringent SNP calling parameters, especially when admixed individuals are included. In contrast, analyses of incomplete but larger datasets converged on the same phylogeny, irrespective of the reconstruction method used or the proportion of missing data. The Alytes tree features three Miocene-diverged clades corresponding to the proposed subgenera Ammoryctis (A. cisternasii), Baleaphryne (A. maurus, A. dickhilleni and A. muletensis), and Alytes (A. obstetricans complex). The latter consists of six evolutionary lineages, grouped into three clades of Pliocene origin, and currently delimited as two species: (1) A. almogavarii almogavarii and A. a. inigoi; (2) A. obstetricans obstetricans and A. o. pertinax; (3) A. o. boscai and an undescribed taxon (A. o. cf. boscai). These results contradict the mitochondrial tree, due to past mitochondrial captures in A. a. almogavarii (central Pyrenees) and A. o. boscai (central Iberia) by A. obstetricans ancestors during the Pleistocene. Patterns of admixture between subspecies appear far more extensive than previously assumed from microsatellites, causing nomenclatural uncertainties, and even underlying the reticulate evolution of one taxon (A. o. pertinax). All Ammoryctis and Baleaphryne species form shallow clades, so their taxonomy should remain stable. Amid the prevalence of cyto-nuclear discordance among terrestrial vertebrates and the usual lack of resolution of conventional nuclear markers, our study advocates for phylogeography based on next-generation sequencing, but also encourages properly exploring parameter space and sampling schemes when building and analyzing genomic datasets.

Higher temperature induces oxidative stress in hybrids but not in parental species: A case study of crested newts

Ectotherms are particularly sensitive to global warming due to their limited capacity to thermoregulate, which can impact their performance and fitness. From a physiological standpoint, higher temperatures often enhance biological processes that can induce the production of reactive oxygen species and result in a state of cellular oxidative stress. Temperature alters interspecific interactions, including species hybridization. Hybridization under different thermal conditions could amplify parental (genetic) incompatibilities, thus affecting a hybrid's development and distribution. Understanding the impact of global warming on the physiology of hybrids and particularly their oxidative status could help in predicting future scenarios in ecosystems and in hybrids. In the present study, we investigated the effect of water temperature on the development, growth and oxidative stress of two crested newt species and their reciprocal hybrids. Larvae of Triturus macedonicus and T. ivanbureschi, and their T. macedonicus-mothered and T. ivanbureschi-mothered hybrids were exposed for 30 days to temperatures of 19°C and 24°C. Under the higher temperature, the hybrids experienced increases in both growth and developmental rates, while parental species exhibited accelerated growth (T. macedonicus) or development (T. ivanbureschi). Warm conditions also had different effects on the oxidative status of hybrid and parental species. Parental species had enhanced antioxidant responses (catalase, glutathione peroxidase, glutathione S-transferase and SH groups), which allowed them to alleviate temperature-induced stress (revealed by the absence of oxidative damage). However, warming induced an antioxidant response in the hybrids, including oxidative damage in the form of lipid peroxidation. These findings point to a greater disruption of redox regulation and metabolic machinery in hybrid newts, which can be interpreted as the cost of hybridization that is likely linked to parental incompatibilities expressed under a higher temperature. Our study aims to improve mechanistic understanding of the resilience and distribution of hybrid species that cope with climate-driven changes.

Phylogeography and Cryptic Species Structure of a Locally Adapted Parasite in New Zealand

Phylogeographic patterns of many taxa on New Zealand's South Island are characterised by disjunct distributions that have been attributed to Pleistocene climatic cycles and the formation of the Southern Alps. Pleistocene glaciation has also been implicated in shaping the contemporary genetic differentiation between populations of the aquatic snail Potamopyrgus antipodarum. We investigated whether similar phylogeographic patterns exist for the snail's locally adapted trematode parasite, Atriophallophorus winterbourni. We found evidence for a barrier to gene-flow in sympatry between cryptic, but ecologically divergent species. When focusing on the most common of these species, disjunct geographic distributions are found for mitochondrial lineages that diverged during the Pleistocene. The boundary between these distributions is found in the central part of the South Island and reinforced by low cross-alpine migration. Further support for a vicariant origin of the phylogeographic pattern was found when assessing nuclear multilocus SNP data. Nuclear and mitochondrial population differentiation was concordant in pattern, except for populations in a potential secondary contact zone. Additionally, we found larger than expected differentiation between nuclear- and mitochondrial-based empirical Bayes F_ST estimates (global F_ST : 0.02 versus 0.39 for nuclear and mitochondrial data, respectively). Population subdivision is theoretically expected to be stronger for mitochondrial genomes due to a smaller effective population size, but the strong difference here, together with mito-nuclear discordance in a putative contact zone, is potentially indicative of divergent gene flow of nuclear and mitochondrial genomes.

The Reproductive Success of Triturus ivanbureschi × T. macedonicus F1 Hybrid Females (Amphibia: Salamandridae)

Simple Summary

Two moderately related large-bodied newt species endemic to the Balkan Peninsula, the Balkan crested newt (Triturus ivanbureschi) and the Macedonian crested newt (T. macedonicus), coexist and hybridize in central Serbia. Many generations of mutual hybrid crossings and backcrossings with parental species shaped the genetic composition of hybrid populations. Natural populations have admixed nuclear DNA (nuDNA) of parental species and T. ivanbureschi mitochondrial DNA (mtDNA), which is usually maternally inherited. The mechanisms that direct gene flow and shape the first generations of hybrids could explain the formation of hybrid zones and their maintenance in nature. We followed and compared life history traits related to reproduction of the first generation of reciprocal hybrids obtained by experimental crossing. Our results suggested that possible incompatibilities between mitochondrial and nuclear genomes, which could lead to the exclusion of T. macedonicus mtDNA in natural populations, most likely act at later stages of development or subsequent hybrid generations. Results from this study add to the growing knowledge of Triturus hybrid biology and ecology, which is the baseline for conservation programs necessary to protect these highly endangered amphibians.

Abstract

Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. Consequences of hybridization upon secondary contact of two species include species displacement and asymmetrical introgression of T. ivanbureschi mtDNA. We set an experimental reciprocal cross of parental species and obtained two genotypes of F₁ hybrids (with T. ivanbureschi or T. macedonicus mtDNA). When hybrids attained sexual maturity, they were engaged in mutual crossings and backcrossing with parental species. We followed reproductive traits over two successive years. Our main aim was to explore the reproductive success of F₁ females carrying different parental mtDNA. Additionally, we tested for differences in reproductive success within female genotypes depending on the crossing with various male genotypes (hybrids or parental species). Both female genotypes had similar oviposition periods, number of laid eggs and hatched larvae but different body and egg sizes. Overall reproductive success (percentage of egg-laying females and viability of embryos) was similar for both genotypes. The type of crossing led to some differences in reproductive success within female genotypes. The obtained results suggest that processes that led to exclusion of T. macedonicus mtDNA in natural populations may be related to the survival at postembryonic stages of F₂ generation or reproductive barriers that emerged in subsequent hybrid generations.

Consequences of hybridization on life history and growth in postmetamorphic Triturus macedonicus

The Macedonian crested newt T. macedonicus forms a complex hybrid zone with the Balkan crested newt T. ivanbureschi in the central part of the Balkan Peninsula. In this study, we compared life history parameters (sex ratio, survival rate and age of sexual maturation) and growth parameters (body length and mass) of T. macedonicus and T. macedonicus × T. ivanbureschi hybrids over the first three postmetamorphic years. Survival rates were high and similar for both genotypes. Sexual dimorphism in body size (length and mass) was evident at the beginning of the third postmetamorphic year, after the first breeding year, for both T. macedonicus and hybrids. We did not find clear and consistent difference in any of the analysed traits suggesting that hybridization with T. ivabureschi does not affect postmetamorphic growth and survival of T. macedonicus.

Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure

Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.

Adaptation of Drosophila subobscura chromosomal inversions to climatic variables: the Balkan natural population of Avala

The adaptive value of chromosomal inversions continues raising relevant questions in evolutionary biology. In many species of the Drosophila genus, different inversions have been recognized to be related to thermal adaptation, but it is necessary to determine to which specific climatic variables the inversions are adaptive. With this aim, the behavior of thermal adapted inversions of Drosophila subobscura regarding climatic variables was studied in the natural population of Avala (Serbia) during the 2014-2017 period. The results obtained were compared with those previously reported in the Font Groga (Barcelona, Spain) population, which presents different climatic and environmental conditions. In both populations, it was observed that most thermal adapted inversions were significantly associated with the first, second or both principal components, which were related with maximum, minimum and mean temperatures. Moreover, a significant increase over years (2004-2017) for the minimum temperature was detected. In parallel, a significant variation over time in Avala was only observed for the frequencies of 'warm' and 'non-thermal' adapted inversions of the U chromosome. However, stability in the chromosomal inversion polymorphism was observed for the 2014-2017 period which might result from the temporal span of the study and/or selective process acting on the population.

Genetic Divergence Across Glacial Refugia Despite Interglacial Gene Flow in a Crested Newt

MtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.

A reassessment of the diversity of green toads (Bufotes) in the circum-Aegean region

The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phylogeographic study based on mitochondrial and microsatellite loci identified the hybrid zone between the European (viridis) and Anatolian (sitibundus) lineages of B. viridis all over the Balkan Peninsula, but subsequent range-wide genomic analyses (>1000 SNPs) located this transition in Turkey, a thousand kilometers eastwards. In order to clarify the diversity and taxonomy of the circum-Aegean populations, we reconciled these conflicting findings by integrating previous data with pure sitibundus individuals. Our results confirmed that the viridis/sitibundus hybrid zone extends in Western Anatolia, but that southeastern European populations feature cytonuclear discordances and a high and structured microsatellite diversity. This remarkable situation may stem from a massive geographic displacement of the hybrid zone during the last glacial fluctuations, an underappreciated yet seemingly common feature among the herpetofauna of the region. Our study thus contributes to the rising view that mitochondrial DNA can be a poor predictor of current phylogeographic structure, hence the need for genomic data, especially for narrowly distributed taxa. Finally, the analyses unambiguously support the distinction of a micro-endemic clade of green toads unique to some Cyclades islands, for which we provide a formal taxonomic description.