Subtle East–West Phylogeographic Break of Asteropyrum (Ranunculaceae) in Subtropical China and Adjacent Areas

East–west phylogeographic break is common among plant species in subtropical China. However, the estimation time of east–west phylogeographic break has always relied on inferences of calibrated phylogenies, and the contribution of environmental heterogeneity to population differentiation has largely been ignored. In this study, we estimated the divergence time of Asteropyrum populations through coalescent-based approaches based on DNA sequences of ten nuclear loci and evaluated the contribution of environmental heterogeneity to population differentiation. The results showed that there were two chloroplast clades and nuclear groups within Asteropyrum, displaying a subtle pattern of east–west differentiation. The divergence time of the two nuclear groups was dated to ~1.2 Ma, which is associated with climate changes during the Mid-Pleistocene transition. A genetic admixture event between the two genetic groups happened at ~0.46 Ma, resulting in several admixed populations. Isolation by environmental distance (IBE) explained the majority (46.32%) of population differentiation, but that isolation by geographic distance (IBD) only contributed 4.66%. The results of this study suggest that climate changes during the Pleistocene may be a major cause for the east–west phylogeographic break in subtropical China. However, the complex terrain and high environmental heterogeneity in the west of subtropical China (and adjacent regions such as the Hengduan Mountains and the Himalayan Moutains) caused by strong geological uplift may have profoundly shaped the population structure of plant species in subtropical China.

Two new frog species from the Litoria rubella species group from eastern Australia

The bleating tree frog (Litoria dentata) is one of the more prominent pelodryadid frogs of eastern Australia by virtue of its extremely loud, piercing, male advertisement call. A member of the Litoria rubella species group, L. dentata has a broad latitudinal distribution and is widespread from coastal and subcoastal lowlands through to montane areas. A recent mitochondrial DNA analysis showed a deep phylogeographic break between populations of L. dentata on the mid-north coast of New South Wales. Here we extended the mitochondrial survey with more geographically comprehensive sampling and tested the systematic implications of our findings with nuclear genome wide single-nucleotide polymorphism, morphological and male advertisement call datasets. While similar in appearance and in male advertisement call, our integrative analysis demonstrates the presence of three species which replace each other in a north-south series. We redescribe Litoria dentata, which is restricted to coastal north-eastern New South Wales, and formally describe Litoria balatus sp. nov., from south-eastern Queensland, and Litoria quiritatus sp. nov., from the mid-coast of New South Wales to north-eastern Victoria.

A metagenomic analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea - Baltic Sea transition zone

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of marine organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about the wrackbed microbiome, its composition, trophic ecology, or how it varies over time and space. Here we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both the wrackbed and seaweed fly microbiomes but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea. These shifts were mostly due to changes in the frequency of different groups of known polysaccharide degraders (Proteobacteria and Bacteroidota). We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the seaweed communities of the North vs. Baltic Sea. Our results reveal the complexities of both the wracked microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?

Aim The evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)—and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR. Location The CFR, located along the southern Cape of South Africa. Methods Published phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not. Results Phylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries. Main conclusions The evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts and test novel hypotheses pertaining to the distribution of genetic diversity among CFR plant taxa. Additionally, the resolution at which CoEs are mapped should be refined, which may provide a valuable tool for future conservation planning and the development of precautionary guidelines for the translocation of genetic material during species reintroductions and commercial cultivation of Cape endemic crops. Thus, to answer the question ‘Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?’—yes, CoEs do appear to be an important tool for Cape phylogeographers. However, the data is limited and more plant phylogeography work is needed in the CFR.

Reduced representation sequencing for symbiotic anthozoans: are reference genomes necessary to eliminate endosymbiont contamination and make robust phylogeographic inference?

Anthozoan cnidarians form the backbone of coral reefs. Their success relies on endosymbiosis with photosynthetic dinoflagellates in the family Symbiodiniaceae. Photosymbionts represent a hurdle for researchers using population genomic techniques to study these highly imperiled and ecologically critical species because sequencing datasets harbor unknown mixtures of anthozoan and photosymbiont loci. Here we use range-wide sampling and a double-digest restriction-site associated DNA sequencing (ddRADseq) of the sea anemone Bartholomea annulata to explore how symbiont loci impact the interpretation of phylogeographic patterns and population genetic parameters. We use the genome of the closely related Exaiptasia diaphana (previously Aiptasia pallida) to create an anthozoan-only dataset from a genomic dataset containing both B. annulata and its symbiodiniacean symbionts and then compare this to the raw, holobiont dataset. For each, we investigate spatial patterns of genetic diversity and use coalescent model-based approaches to estimate demographic history and population parameters. The Florida Straits are the only phylogeographic break we recover for B. annulata, with divergence estimated during the last glacial maximum. Because B. annulata hosts multiple members of Symbiodiniaceae, we hypothesize that, under moderate missing data thresholds, de novo clustering algorithms that identify orthologs across datasets will have difficulty identifying shared non-coding loci from the photosymbionts. We infer that, for anthozoans hosting diverse members of Symbiodinaceae, clustering algorithms act as de facto filters of symbiont loci. Thus, while at least some photosymbiont loci remain, these are swamped by orders of magnitude greater numbers of anthozoan loci and thus represent genetic “noise,” rather than contributing genetic signal.

Systematics of the combtooth blenny clade Omobranchus (Blenniidae: Omobranchini), with notes on early life history stages

The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.

Repeated expansions and fragmentations linked to Pleistocene climate changes shaped the genetic structure of a woody climber,Actinidia arguta(Actinidiaceae)

The genetic structure of temperate plants was extremely affected by climate changes during the Pleistocene. In East Asia, however, there are a limited number of phylogeography studies of widely distributed species. Actinidia arguta (Sieb. & Zucc.) Planch. ex Miq. (Actinidiaceae), a widely distributed woody climber, was chosen for this study. Twelve haplotypes were obtained using five chloroplast fragments. No haplotypes were shared on two sides of the Qinling–Dabie mountain ranges, indicating a phylogeographic break. The break was further revealed by analysis of molecular variance, spatial analysis of molecular variance, and ecological niche modelling. The most recent common ancestor of all haplotypes showed that global cooling and aridity of the Asian interior at the Pliocene–Pleistocene boundary may triggered this divergence. Two monophyletic lineages (north and south lineage) were revealed by Bayesian phylogeny and the maximum parsimony network. In the north lineage, mismatch analysis indicated an ancient spatial expansion. Distant distribution of closely related haplotypes indicated subsequent allopatric fragmentation. The widespread haplotype H2 implied another significant range expansion. In the south lineage, a considerable rise in sea level of the East China Sea may have triggered population fragmentation. The nested clade analysis also indicated that expansion and allopatric fragmentation were the main processes shaping the haplotype distributions. So, repeated range expansions and fragmentations have shaped the present genetic structure of A. arguta.