Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

Patterns of Change in Nucleotide Diversity Over Gene Length

Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.

Patterns of change in nucleotide diversity over gene length

Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site (TIS) of a gene. The degree of reduction in diversity at the TIS and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of fast-growth adaptations such as the avoidance of mRNA secondary structure around TIS, the number of rRNAs, and relative codon usage of ribosomal genes. Thus, the dependence of nucleotide diversity on gene length is governed by a combination of selective and non-selective processes. These results have implications for the estimation of effective population size and relative mutation rates based on "silent-site" diversity, and for pN/pS-based prediction of genes under selection.

Speciation without gene-flow in hybridizing deer

Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Hybridisation is part of this continuum and can both promote and inhibit the speciation process. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridizing sister species. We quantified genome-wide historical introgression and performed genome scans to look for signatures of four different selection scenarios. Despite ample modern evidence of hybridisation, we found negligible patterns of ancestral introgression and no signatures of divergence with gene flow, rather localized patterns of allopatric and balancing selection were detected across the genome. Genes under balancing selection were related to immunity, MHC and sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of historical gene-flow suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene and genome wide differentiation accrued via genetic drift. Dobzhansky-Muller incompatibilities and selection against hybrids are hypothesised to be acting, and diversity correlations to recombination rates suggests these sister species are far along the speciation continuum.

Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome

Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets. To address these challenges, we developed target capture probes for genomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built the general purpose bioinformatic pipeline CaptureAl. Phylogenomic analyses of Malagasy Dalbergia species yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatic resources, including the Fabaceae1005 and Dalbergia2396 probe sets, will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

Origin and diversification of the saguaro cactus (Carnegiea gigantea): a within-species phylogenomic analysis

Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulf of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro's current range reflects post-glacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects.

Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae)

The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with "Hastatae clade" sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.

Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species

Phylogeographic studies can uncover robust details about the population structure, demographics, and diversity of species. The smooth greensnake, Opheodrys vernalis, is a small, cryptic snake occupying mesic grassland and sparsely wooded habitats. Although O. vernalis has a wide geographical range, many metapopulations are patchy and some are declining. We used mitochondrial DNA and double digest restriction-site associated DNA sequencing to construct the first phylogeographic assessment of O. vernalis. Genomic analysis of 119 individuals (mitochondrial DNA) and a subset of another 45 smooth greensnakes (nuclear DNA; N = 3031 single nucleotide polymorphisms) strongly supports two longitudinally separated lineages, with admixture in the Great Lakes region. Post-Pleistocene secondary contact best explains admixture from populations advancing northwards. Overall, populations expressed low heterozygosity, variable inbreeding rates, and moderate to high differentiation. Disjunct populations in the Rocky Mountains and central Great Plains regions might be contracting relicts, whereas northerly populations in more continuous mesic habitats (e.g., Prairie Pothole region, southern Canada) had signals of population expansion. Broadly, conservation management efforts should be focused on local populations, because habitat connectivity may facilitate gene flow and genetic diversity.

Spatial Genetic Structure of Prunus mongolica in Arid Northwestern China Based on RAD Sequencing Data

The extensive range of sand deserts, gravel deserts, and recent human activities have shaped habitat fragmentation of relict and endangered plants in arid northwestern China. Prunus mongolica is a relict and endangered shrub that is mainly distributed in the study area. In the present study, population genomics was integrated with a species distribution model (SDM) to investigate the spatial genetic diversity and structure of P. mongolica populations in response to habitat fragmentation and create a proposal for the conservation of this endangered species. The results showed that the northern marginal populations were the first isolated from other populations. The SDM suggested that these marginal populations had low levels of habitat suitability during the glacial period. They could not obtain migration corridors, and thus possessed low levels of gene flow connection with other populations. Additionally, several populations underwent secondarily geographical isolation from other central populations, which preserved particular genetic lineages. Genetic diversity was higher in southern populations than in northern ones. It was concluded that long-term geographical isolation after historical habitat fragmentation promoted the divergence of marginal populations and refugial populations along mountains from other populations. The southern populations could have persisted in their distribution ranges and harbored higher levels of genetic diversity than the northern populations, whose distribution ranges fluctuated in response to paleoclimatic changes. We propose that the marginal populations of P. mongolica should be well considered in conservation management.

The Rapid Rise of Next-Generation Natural History

Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages

While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.

An escape-to-radiate model for explaining the high plant diversity and endemism in campos rupestres†

With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.

Phylogeographic structure of the dunes sagebrush lizard, an endemic habitat specialist

Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits in evolutionary divergence and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of S. arenicolus. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of S. arenicolus.

Genomic Phylogeography of Gymnocarpos przewalskii (Caryophyllaceae): Insights into Habitat Fragmentation in Arid Northwestern China

Extensive range of deserts and gobis (rocks) had promoted habitat fragmentation of species in arid northwestern China. Distribution of endangered Gymnocarpos przewalskii Maxim. covers most of gobis (rocks) and desert terrain across arid regions of northwestern China. In the present study, we had employed genomic phylogeographical analysis to investigate population structure of G. przewalskii and test the effect of environmental conditions on spatial pattern of genetic diversity. Results showed four groups were identified from east to west: Edge of the Alxa Desert, Hexi Corridor, Hami Basin, and North edge of the Tarim Basin. Genetic diversity was at an equal level among four groups. General linear model (GLM) analysis showed spatial pattern of genetic diversity was significant correlated with three habitat variables including habitat suitability at present (Npre) and last glacial maximum (LGM) (NLGM) periods, and locality habitat stability (NStab). It concluded that habitat fragmentation had triggered lineage divergences of G. przewalskii in response to long-term aridification. Genome-wide single nucleotide polymorphisms (SNPs) could increase the ability of clarifying population structures in comparison with traditional molecular markers. Spatial pattern of genetic diversity was determined by fragmented habitats with high habitat suitability (Npre and NLGM) and stability (NStab). At last, we propose to establish four conservation units which are in consistent with the population grouping to maintain the genetic integrity of this endangered species.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

Speciation genes are more likely to have discordant gene trees

Speciation genes are responsible for reproductive isolation between species. By directly participating in the process of speciation, the genealogies of isolating loci have been thought to more faithfully represent species trees. The unique properties of speciation genes may provide valuable evolutionary insights and help determine the true history of species divergence. Here, we formally analyze whether genealogies from loci participating in Dobzhansky-Muller (DM) incompatibilities are more likely to be concordant with the species tree under incomplete lineage sorting (ILS). Individual loci differ stochastically from the true history of divergence with a predictable frequency due to ILS, and these expectations-combined with the DM model of intrinsic reproductive isolation from epistatic interactions-can be used to examine the probability of concordance at isolating loci. Contrary to existing verbal models, we find that reproductively isolating loci that follow the DM model are often more likely to have discordant gene trees. These results are dependent on the pattern of isolation observed between three species, the time between speciation events, and the time since the last speciation event. Results supporting a higher probability of discordance are found for both derived-derived and derived-ancestral DM pairs, and regardless of whether incompatibilities are allowed or prohibited from segregating in the same population. Our overall results suggest that DM loci are unlikely to be especially useful for reconstructing species relationships, even in the presence of gene flow between incipient species, and may in fact be positively misleading.

Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data

Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.

Reticulation, divergence, and the phylogeography-phylogenetics continuum

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.

Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice. By comparing the louse and ground-dove phylogenies, we found that over long-term evolutionary scales their phylogenies were largely congruent. Many louse lineages (both species and populations) also demonstrated high host-specificity, suggesting ground-dove divergence is a primary driver of their parasites' diversity. However, the few louse taxa that are generalists are structured according to biogeography at the population level. This suggests dispersal among sympatric hosts has some effect on body louse diversity, but over deeper time scales the parasites eventually sort according to host species. Overall, our results demonstrate that multiple factors explain the patterns of diversity in this group of parasites, and that the effects of these factors can vary over different evolutionary scales. The integrative approach we employed was crucial for uncovering these patterns, and should be broadly applicable to other studies.

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

Ongoing elimination efforts have altered the global distribution of Onchocerca volvulus, the agent of river blindness, and further population restructuring is expected as efforts continue. Therefore, a better understanding of population genetic processes and their effect on biogeography is needed to support elimination goals. We describe O. volvulus genome variation in 27 isolates from the early 1990s (before widespread mass treatment) from four distinct locales: Ecuador, Uganda, the West African forest and the West African savanna. We observed genetic substructuring between Ecuador and West Africa and between the West African forest and savanna bioclimes, with evidence of unidirectional gene flow from savanna to forest strains. We identified forest:savanna-discriminatory genomic regions and report a set of ancestry informative loci that can be used to differentiate between forest, savanna and admixed isolates, which has not previously been possible. We observed mito-nuclear discordance possibly stemming from incomplete lineage sorting. The catalogue of the nuclear, mitochondrial and endosymbiont DNA variants generated in this study will support future basic and translational onchocerciasis research, with particular relevance for ongoing control programmes, and boost efforts to characterize drug, vaccine and diagnostic targets.

Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes

OBJECTIVES

Two subgroups make up the marmoset genus Callithrix. The "aurita" group is composed of two species, whereas evolutionary relationships among the four species of the "jacchus" group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group.

MATERIALS AND METHODS

MtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference.

RESULTS

In our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA.

DISCUSSION

Callithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses.

Ephemeral ecological speciation and the latitudinal biodiversity gradient

The richness of biodiversity in the tropics compared to high-latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High-latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of "environmental harshness" and "hard selection" as eco-evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity.

In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex

Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent-based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein-coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.

Caenorhabditis evolution in the wild

Recent research has filled many gaps about Caenorhabditis natural history, simultaneously exposing how much remains to be discovered. This awareness now provides means of connecting ecological and evolutionary theory with diverse biological patterns within and among species in terms of adaptation, sexual selection, breeding systems, speciation, and other phenomena. Moreover, the heralded laboratory tractability of C. elegans, and Caenorhabditis species generally, provides a powerful case study for experimental hypothesis testing about evolutionary and ecological processes to levels of detail unparalleled by most study systems. Here, I synthesize pertinent theory with what we know and suspect about Caenorhabditis natural history for salient features of biodiversity, phenotypes, population dynamics, and interactions within and between species. I identify topics of pressing concern to advance Caenorhabditis biology and to study general evolutionary processes, including the key opportunities to tackle problems in dispersal dynamics, competition, and the dimensionality of niche space.

Multilocus species trees show the recent adaptive radiation of the mimetic heliconius butterflies

Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 myr, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

Background

High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.

Results

Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.

Conclusions

Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0318-0) contains supplementary material, which is available to authorized users.

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.

Assessing the phylogeographic history of the montane caddisfly Thremma gallicum using mitochondrial and restriction-site-associated DNA (RAD) markers

Repeated Quaternary glaciations have significantly shaped the present distribution and diversity of several European species in aquatic and terrestrial habitats. To study the phylogeography of freshwater invertebrates, patterns of intraspecific variation have been examined primarily using mitochondrial DNA markers that may yield results unrepresentative of the true species history. Here, population genetic parameters were inferred for a montane aquatic caddisfly, Thremma gallicum, by sequencing a 658-bp fragment of the mitochondrial CO1 gene, and 12,514 nuclear RAD loci. T. gallicum has a highly disjunct distribution in southern and central Europe, with known populations in the Cantabrian Mountains, Pyrenees, Massif Central, and Black Forest. Both datasets represented rangewide sampling of T. gallicum. For the CO1 dataset, this included 352 specimens from 26 populations, and for the RAD dataset, 17 specimens from eight populations. We tested 20 competing phylogeographic scenarios using approximate Bayesian computation (ABC) and estimated genetic diversity patterns. Support for phylogeographic scenarios and diversity estimates differed between datasets with the RAD data favouring a southern origin of extant populations and indicating the Cantabrian Mountains and Massif Central populations to represent highly diverse populations as compared with the Pyrenees and Black Forest populations. The CO1 data supported a vicariance scenario (north-south) and yielded inconsistent diversity estimates. Permutation tests suggest that a few hundred polymorphic RAD SNPs are necessary for reliable parameter estimates. Our results highlight the potential of RAD and ABC-based hypothesis testing to complement phylogeographic studies on non-model species.

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome.

Specialist versus generalist life histories and nucleotide diversity in Caenorhabditis nematodes

Species with broad ecological amplitudes with respect to a key focal resource, niche generalists, should maintain larger and more connected populations than niche specialists, leading to the prediction that nucleotide diversity will be lower and more subdivided in specialists relative to their generalist relatives. This logic describes the specialist-generalist variation hypothesis (SGVH). Some outbreeding species of Caenorhabditis nematodes use a variety of invertebrate dispersal vectors and have high molecular diversity. By contrast, Caenorhabditis japonica lives in a strict association and synchronized life cycle with its dispersal host, the shield bug Parastrachia japonensis, itself a diet specialist. Here, we characterize sequence variation for 20 nuclear loci to investigate how C. japonica's life history shapes nucleotide diversity. We find that C. japonica has more than threefold lower polymorphism than other outbreeding Caenorhabditis species, but that local populations are not genetically disconnected. Coupled with its restricted range, we propose that its specialist host association contributes to a smaller effective population size and lower genetic variation than host generalist Caenorhabditis species with outbreeding reproductive modes. A literature survey of diverse organisms provides broader support for the SGVH. These findings encourage further testing of ecological and evolutionary hypotheses with comparative population genetics in Caenorhabditis and other taxa.