Cytonuclear discordance across a leopard frog contact zone

Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia)

Paleo-climatic fluctuations have driven episodic changes in species distributions, providing opportunities for populations to diverge in isolation and hybridise following secondary contact. Studies of phylogeographic diversity and patterns of gene flow across hybrid zones can provide insight into contemporary species boundaries and help to inform taxonomic and conservation inferences. Here we explore geographic diversity within the acoustically divergent yet morphologically conserved south-eastern Australian smooth frog complex and assess gene flow across a narrow hybrid zone using mitochondrial nucleotide sequences and nuclear genome-wide single nucleotide polymorphisms. Our analyses reveal the presence of an evolutionarily distinct taxon restricted to the Otway Plains and Ranges, Victoria, which forms a narrow (9-30 km wide), spatiotemporally stable (>50 years) hybrid zone with Geocrinia laevis, which we describe herein as a new species.

Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts

Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.

Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs

Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.

Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China's mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species Dipteronia sinensis in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced-genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that D. sinensis could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of D. sinensis occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation-with-migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for D. sinensis in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.

Phylogenetics and phylogeography of a long-legged harvestman (Arachnida : Opiliones) in the Brazilian Atlantic Rain Forest reveals poor dispersal, low diversity and extensive mitochondrial introgression

We used DNA sequence data to test the morphology-based taxonomy and examine the biogeography of the Brazilian Atlantic Rain Forest genus Promitobates. Most species are well differentiated morphologically, and a previous morphological phylogeny recovered the genus as monophyletic. However, some of these species have overlapping geographical distributions and considerable intraspecific variation, perhaps representing a species complex. Mitochondrial (12S rRNA and COI) and nuclear (ITS2 and 28S) genes were sequenced from 132 specimens collected from 27 localities. The results are consistent with significant mitochondrial introgression among the species P. ornatus, P. hatschbachi, P. lager, P. bellus and P. intermedius (the ‘P. ornatus species complex’), with one specimen identified as a hybrid between P. nigripes and this complex. A phylogeographic study of the complex was conducted using mitochondrial haplotypes. This revealed remarkably poor dispersal among populations, with only one case of a shared haplotype, and very low genetic diversity. The phylogeny showed a clear break between populations on either side of a narrow region of forest, suggesting an important historical event separated these lineages in the genus. The analyses also pointed to population breaks that date back several millions of years or extremely small effective population sizes, depending on the mutation rate.

Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.

Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.)

Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (structure), bidirectional estimates of gene flow (migrate-n and IMa2) and phylogeny-based methods (*beast, bucky) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.

Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data

Background

Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC).

Results

We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression.

Conclusions

Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.

A new species of leopard frog (Anura: Ranidae) from the urban northeastern US

Past confusion about leopard frog (genus Rana) species composition in the Tri-State area of the US that includes New York (NY), New Jersey (NJ), and Connecticut (CT) has hindered conservation and management efforts, especially where populations are declining or imperiled. We use nuclear and mitochondrial genetic data to clarify the identification and distribution of leopard frog species in this region. We focus on four problematic frog populations of uncertain species affiliation in northern NJ, southeastern mainland NY, and Staten Island to test the following hypotheses: (1) they are conspecific with Rana sphenocephala or R. pipiens, (2) they are hybrids between R. sphenocephala and R. pipiens, or (3) they represent one or more previously undescribed cryptic taxa. Bayesian phylogenetic and cluster analyses revealed that the four unknown populations collectively form a novel genetic lineage, which represents a previously undescribed cryptic leopard frog species, Rana sp. nov. Statistical support for R. sp. nov. was strong in both the Bayesian (pp=1.0) and maximum-likelihood (bootstrap=99) phylogenetic analyses as well as the Structure cluster analyses. While our data support recognition of R. sp. nov. as a novel species, we recommend further study including fine-scaled sampling and ecological, behavioral, call, and morphological analyses before it is formally described.

Phylogeography of the marine macroalga Sargassum hemiphyllum (Phaeophyceae, Heterokontophyta) in northwestern Pacific

Sargassum hemiphyllum is commonly found in Japan and Korea, with a variety, var. chinense, that is found distributed in the southern Chinese coast. We previously reported distinct genetic differentiation between the two taxa based on the PCR-RFLP data of plastid RubiscoL-S spacer. The present study aims at elucidating the phylogeographic pattern of S. hemiphyllum based on more markers in the nuclear and extranuclear genomes, with a view to reveal the occurrence of hybridization. The two allopatrically distributed taxa were found to be genetically distinct in nuclear ITS2, plastidial Rubisco (Rbc) and mitochondrial TrnW_I (Trn) spacers. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the late Miocene (6.58-11.25 Mya). Divergence within both S. hemiphyllum and the chinense variety was observed based on Trn spacer, while the divergence in S. hemiphyllum was further confirmed in Rbc spacer. This divergence appears to correspond to the separation of the Japanese populations between the Sea of Japan and the Pacific that occurred around 0.92-2.88 Mya (the early Pleistocene). The presence of an ITS2 clone resembling var. chinense sequences in a Japanese population of S. hemiphyllum (JpNS) raises the possibility of the introgression of var. chinense individuals into S. hemiphyllum population. Compared to that between S. hemiphyllum and the chinense variety, hybridization among the Japanese and Korean populations of S. hemiphyllum is highly probable as all these individuals share a pool of nuclear ITS2 sequences, possibly attributable to incomplete concerted evolution of ITS2.

The cause of global amphibian declines: a developmental endocrinologist's perspective

Greater than 70% of the world's amphibian species are in decline. We propose that there is probably not a single cause for global amphibian declines and present a three-tiered hierarchical approach that addresses interactions among and between ultimate and proximate factors that contribute to amphibian declines. There are two immediate (proximate) causes of amphibian declines: death and decreased recruitment (reproductive failure). Although much attention has focused on death, few studies have addressed factors that contribute to declines as a result of failed recruitment. Further, a great deal of attention has focused on the role of pathogens in inducing diseases that cause death, but we suggest that pathogen success is profoundly affected by four other ultimate factors: atmospheric change, environmental pollutants, habitat modification and invasive species. Environmental pollutants arise as likely important factors in amphibian declines because they have realized potential to affect recruitment. Further, many studies have documented immunosuppressive effects of pesticides, suggesting a role for environmental contaminants in increased pathogen virulence and disease rates. Increased attention to recruitment and ultimate factors that interact with pathogens is important in addressing this global crisis.

A revised leopard frog phylogeny allows a more detailed examination of adaptive evolution at ranatuerin-2 antimicrobial peptide loci

Ranatuerins are antimicrobial peptides of the innate immune system found in ranid frogs. We previously presented evidence that a positive selective sweep had fixed a single allele at the Ranatuerin2 locus in the northern leopard frog (Rana pipiens). In this paper, we further investigate the evolutionary history of ranatuerins as follows. First, we sequenced Ranatuerin2 in additional individuals of R. pipiens and related frog species and compared diversity and divergence at these sequences with that at four putatively neutrally evolving loci. Second, we asked whether the evolutionary patterns observed at Ranatuerin2 were typical for ranatuerin loci by sequencing our samples at a paralogous locus, Ranatuerin2b, and performing the same neutrality tests. Ranatuerin2b also showed strong and significant evidence of at least one selective sweep. Third, we used the neutral loci to independently resolve conflicting hypotheses about phylogenetic relationships among our study species. Both the neutral loci and the ranatuerin loci supported an older phylogeny inferred from allozyme data and strongly rejected a more recent phylogeny inferred from mitochondrial DNA. Finally, in order to test whether the sweep was driven by the evolution of substantially new peptide function, we used the phylogeny to reconstruct the hypothetical Ranatuerin2 peptide that existed before the sweep. We synthesized this peptide and tested its activity and that of the extant peptide against six bacterial pathogens of frogs. We observed antibacterial activity but found no significant functional differences between the two peptides.

Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in populations of deer mice (Peromyscus maniculatus)

We investigated a major geographic break in mitochondrial DNA (mtDNA) haplotypes in deer mice, Peromyscus maniculatus, by analysing spatial variation in a 491-bp fragment of the mtDNA control region from 455 samples distributed across a north-south transect of 2000 km in Western North America. To determine whether the mtDNA break was reflected in the nuclear genome, we then compared spatial variation in 13 nuclear microsatellites of 95 individuals surrounding the mtDNA break. Using a canonical correlation analysis we found that nuclear genomic variation was not correlated with mtDNA differentiation. The contrasting patterns of variation in mtDNA and nuclear DNA are consistent with a hypothesis of historic genetic drift that occurred in isolated refugia combined with recent gene flow between the formerly isolated refugial populations. A Mantel test of genetic vs. geographic distance revealed that recent gene flow between deer mouse populations has been high. We conclude that past vicariant events associated with Pleistocene climate changes together with recent gene flow have created the observed intra-specific cytonuclear discordance in Western North America.

Toward understanding the distribution of Laurasian frogs: a test of Savage's biogeographical hypothesis using the genus Bombina

Several anuran groups of Laurasian origin are each co-distributed in four isolated regions of the Northern Hemisphere: central/southern Europe and adjacent areas, Korean Peninsula and adjacent areas, Indo-Malaya, and southern North America. Similar distribution patterns have been observed in diverse animal and plant groups. Savage [Savage, J.M., 1973. The geographic distribution of frogs: patterns and predictions. In: Vial, J.L. (Ed.), Evolutionary Biology of the Anurans. University of Missouri Press, Columbia, pp. 351-445] hypothesized that the Miocene global cooling and increasing aridities in interiors of Eurasia and North America caused a southward displacement and range contraction of Laurasian frogs (and other groups). We use the frog genus Bombina to test Savage's biogeographical hypothesis. A phylogeny of Bombina is reconstructed based on three mitochondrial and two nuclear gene fragments. The genus is divided into three major clades: an Indo-Malaya clade includes B. fortinuptialis, B. lichuanensis, B. maxima, and B. microdeladigitora; a European clade includes B. bombina, B. pachypus, and B. variegata; and a Korean clade contains B. orientalis. The European and Korean clades form sister-group relationship. Molecular dating of the phylogenetic tree using the penalized likelihood and Bayesian analyses suggests that the divergence between the Indo-Malaya clade and other Bombina species occurred 5.9-28.6 million years ago. The split time between the European clade and the Korean clade is estimated at 5.1-20.9 million years ago. The divergence times of these clades are not significantly later than the timing of Miocene cooling and drying, and therefore can not reject Savage's hypothesis. Some other aspects of biogeography of Bombina also are discussed. The Korean Peninsula and the Shandong Peninsula might have supplied distinct southern refugia for B. orientalis during the Pleistocene glacial maxima. In the Indo-Malaya clade, the uplift of the Tibetan Plateau might have promoted the split between B. maxima and the other species.

Balancing selection at a frog antimicrobial peptide locus: fluctuating immune effector alleles?

Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host–pathogen coevolution and the ability of species to resist disease epidemics.