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Systematics and biogeography of the whistlers (Aves: Pachycephalidae) inferred from ultraconserved elements and ancestral area reconstruction
Abstract
The utility of islands as natural laboratories of evolution is exemplified in the patterns of differentiation in widespread, phenotypically variable lineages. The whistlers (Aves: Pachycephalidae) are one of the most complex avian radiations, with a combination of widespread and locally endemic taxa spanning the vast archipelagos of the Indo-Pacific, making them an ideal group to study patterns and processes of diversification on islands. Here, we present a robust, species-level phylogeny of all five genera and 85% of species within Pachycephalidae, based on thousands of ultraconserved elements (UCEs) generated with a target-capture approach and high-throughput sequencing. We clarify phylogenetic relationships within Pachycephala and report on divergence timing and ancestral range estimation. We explored multiple biogeographic coding schemes that incorporated geological uncertainty in this complex region. The biogeographic origin of this group was difficult to discern, likely owing to aspects of dynamic Earth history in the Indo-Pacific. The Australo-Papuan region was the likely origin of crown-group whistlers, but the specific ancestral area could not be identified more precisely than Australia or New Guinea, and Wallacea may have played a larger role than previously realized in the evolutionary history of whistlers. Multiple independent colonizations of island archipelagos across Melanesia, Wallacea, and the Philippines contributed to the relatively high species richness of extant whistlers. This work refines our understanding of one of the regions’ most celebrated bird lineages and adds to our growing knowledge about the patterns and processes of diversification in the Indo-Pacific.
... Technologies such as restriction site-associated DNA sequencing (RADseq), double digest RAD sequencing (ddRADseq), genotype-by-sequencing (GBS), and target capture of ultraconserved elements (UCEs) have produced data on thousands of anonymous regions in many avian genomes. These genomic data sets have informed us about complex evolutionary histories (Stervander et al. 2015;Oliveros et al. 2021;Brady et al. 2022;McCullough et al. 2022), introgressive hybridization Stervander et al. 2022), and dynamics of population structure and gene flow ). In addition, they have been used in genome-wide association studies (GWAS) to identify genes under selection (Chaves et al. 2016;Armstrong et al. 2018;Bourgeois et al. 2020;Gabrielli et al. 2020;Martin et al. 2021). ...
... The data in the present study do not allow us to decipher these aspects of phylogenomic study design because we designed our experiment as a heterogeneous mix of samples with different properties. This is intended to mirror current practice, as combining data from different sources is a common avenue to increase taxon density and integrate previously published research (e.g., Brady et al., 2022;Forthman et al., 2020;Sless et al., 2022;Williams et al., 2022). Interestingly, the varying performance of the assembly approaches for individual samples highlights the possibility of combining assemblies based on favourable properties. ...
Sequence data assembly is a foundational step in high‐throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under‐studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE‐only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided‐assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia . We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better‐performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
White‐eyes are an iconic avian radiation of small passerines that are mainly distributed across the Eastern Hemisphere tropics and subtropics. Species diversity of white‐eyes is particularly high on oceanic islands, and many species are restricted to single islands or island groups. The high rate of species diversification of white‐eyes ranks them among the fastest radiations known in birds, but whether their accelerated diversification was the result of repeatedly colonizing islands remains unexplored. We used a newly estimated timetree for nearly all zosteropids and phylogenetic comparative methods to estimate and compare diversification rates between island and continental lineages. We show that island white‐eyes have similar extinction rates, yet higher speciation rates compared to continental white‐eyes. In addition, we find higher rates of transitions from islands to continents. Our results show the importance of islands, such as Wallacean and Melanesian archipelagos of the Indo‐Pacific, in facilitating high rates of speciation within this remarkable clade.
The Western Whistler Pachycephala occidentalis Ramsay, 1878, endemic to south-western Western Australia, is almost phenotypically identical with P. pectoralis fuliginosa, the westernmost of six subspecies of Golden Whistler P. pectoralis on Australia and its islands. New mitochondrial DNA (mtDNA) sequence data affirm multiple prior studies in aligning P. pectoralis fuliginosa with other subspecies of P. pectoralis, not P. occidentalis. Conversely, principal coordinates and phylogenetic analyses of new data from >17,000 single nucleotide polymorphisms show P. occidentalis and P. pectoralis fuliginosa barely differentiated from each other, neither being close to any P. pectoralis subspecies. In earlier work, weak, ambiguous signal in nuclear DNA sequences possibly suggested close relationship between P. occidentalis and P. pectoralis fuliginosa but was ‘swamped’ by the phylogenetic signal of the mtDNA. Accordingly, we recognise one species, P. fuliginosa Vigors and Horsfield, 1827, having two subspecies P. fuliginosa occidentalis and P. fuliginosa fuliginosa. Western Whistler remains an appropriate English name for the species P. fuliginosa. MtDNA of Golden Whistler P. pectoralis is hypothesised to have introgressed westwards into the range of P. fuliginosa fuliginosa but not further west into P. fuliginosa occidentalis and we address this. Our conclusions open questions for the conservation of the Western Whistler, now known to have a greater breeding range spanning drier parts of South Australia and Victoria and, potentially, western New South Wales where its occurrence is still unproven. For example, what are the extents of seasonal range overlap, intergradation and niche differentiation of Golden and Western Whistlers in south-eastern Australia and of the two subspecies of Western Whistler?
Wallace's Line demarcates the transition between the differentiated regional faunas of Asia and Australia. However, while patterns of biotic differentiation across these two continental landmasses and the intervening island groups (Wallacea) have been extensively studied, patterns of long-term dispersal and diversification across this region are less well understood. Frogmouths (Aves: Podargidae) are a relictual family of large nocturnal birds represented by three extant genera occurring, respectively, in Asia, 'Sahul' (Australia and New Guinea) and the Solomon Islands, thus spanning Wallace's Line. We used new mitochondrial genomes from each of the extant frogmouth genera to estimate the timeline of frogmouth evolution and dispersal across Wallace's Line. Our results suggest that the three genera diverged and dispersed during the mid-Cenozoic between approximately 30 and 40 Mya. These divergences are among the oldest inferred for any trans-Wallacean vertebrate lineage. In addition, our results reveal that the monotypic Solomons frogmouth (Rigidipenna inexpectata) is one of the most phylogenetically divergent endemic bird lineages in the southwest Pacific. We suggest that the contemporary distribution of exceptionally deep divergences among extant frogmouth lineages may be explained by colonization of, and subsequent long-term persistence on, island arcs in the southwest Pacific during the Oligocene. These island arcs may have provided a pathway for biotic dispersal out of both Asia and Australia that preceded the formation of extensive emergent landmasses in Wallacea by at least 10 million years.
The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes-the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.
Motivation:
Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.
Results:
We present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.
Availability:
The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/.
Supplementary information:
Supplementary data are available at Bioinformatics online.
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.
Background:
Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.
Results:
We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). ASTRAL-III limits the bipartition constraint set (X) to grow at most linearly with n and k. Moreover, it handles polytomies more efficiently than ASTRAL-II, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. The asymptotic running time of ASTRAL-III in the presence of polytomies is [Formula: see text] where D=O(nk) is the sum of degrees of all unique nodes in input trees. The running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. In extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. We observe on a biological avian phylogenomic dataset of 14K genes that contracting low support branches greatly improve results.
Conclusions:
ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species. With ASTRAL-III, low support branches can be removed, resulting in improved accuracy.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
Aim: We derive a new phylogenetic framework of the Indo-Pacific avian genus Edolisoma based on a dense taxon sampling and use it in an explicit spatiotemporal framework to understand the history of intraspecific diversification dynamics in a ‘great speciator’, the Cicadabird Edolisoma tenuirostre/remotum complex.
Location: The Indo-Pacific island region, Australia and New Guinea.
Taxon: Corvoid passerine birds (Passeriformes).
Methods: We used Bayesian phylogenetic methods (beast) to construct a time-calibrated molecular phylogeny of all 19 species in the genus Edolisoma and 27 of 29 subspecies of the E. tenuirostre/remotum complex (previously Coracina tenuirostris) primarily based on one mitochondrial DNA marker. Ancestral area reconstruction methods (‘BioGeoBEARS’) were used to infer the historical biogeography of the genus. We used population-level analyses to assess intraspecific phylogeography and a molecular species delimitation test to evaluate the current taxonomy. A morphometric dataset was used to discuss differential dispersal ability among taxa.
Results: Edolisoma originated in the late Miocene and diversification within the E. tenuirostre/remotum complex began in the Pleistocene. Within the North Melanesian and North Wallacean archipelagos, which have experienced several waves of diversification, we find significant patterns of genetic isolation by distance, but not within the Australo-Papuan ‘mainland’, which was recently back-colonized from these archipelagos. Based on the phylogeny, we suggest several taxonomic changes. We also discuss evidence of taxon cycles within Edolisoma based on correlations of species age, elevational ranges and dispersal ability.
Main conclusions: The biogeographical history and patterns of differentiation between phylogroups within E. tenuirostre support the importance of barriers to gene flow in island systems. Examples of both recent genetic exchange across significant sea barriers and differentiation across much smaller water gaps suggest complex dispersal and diversification dynamics. The capacity for dispersal away from islands, and gradual shifts in dispersal ability in relation to the geographical setting, is supported as important factors in generating a ‘great speciator’.
Aim
Kingfishers are the most species‐rich family in the avian order, Coraciiformes. Their modern distribution is largely pantropical; however, global species diversity is unevenly distributed. For example, 19 of the 114 kingfisher species occur in New Guinea, whereas only six species occur in the entire New World. This disparity in diversity suggests regions with high species richness could represent the ancestral range of the family. Furthermore, some clades of kingfishers ( Ceyx , Todiramphus ) are thought to be the product of rapid insular radiations. Here, we investigated the biogeographical history and speciation dynamics of the Alcedinidae using a fully sampled molecular phylogeny.
Location
Global.
Taxon
Kingfishers (Aves: Coraciiformes: Alcedinidae).
Methods
We inferred a time‐calibrated, species‐level phylogeny of kingfishers from DNA sequences. Our data set comprised up to five Sanger‐sequenced gene regions for all species (one mitochondrial, one nuclear exon and three nuclear introns), plus genus‐level sampling of thousands of ultraconserved elements. We estimated ancestral ranges of kingfishers and explored macroevolutionary rate shifts and diversification rates across the phylogeny.
Results
We recovered a well‐supported phylogeny of kingfishers that includes 34 species whose phylogenetic relationships were not previously known. The pygmy‐kingfishers (subfamily Alcedininae) sit on a long branch, sister to all other kingfishers: subfamilies Cerylinae and Halcyoninae. Crown‐group kingfishers originated in the Indomalayan region approximately 27 Ma with subsequent colonizations into Africa (six times), the New World (twice) and Australasia (representing several major radiations).
Main conclusions
Oceanic islands of Wallacea, the Philippines and Oceania promoted multiple, independent radiations in three species‐rich genera: Ceyx , Actenoides and Todiramphus . In particular, Todiramphus showed patterns consistent with explosive and recent diversification relative to the background speciation rate of non‐ Todiramphus kingfishers, which we attribute to recent colonization of the vast archipelagos of Wallacea and the Pacific.
The archipelagos that form the transition between Asia and Australia were immortalized by Alfred Russel Wallace's observations on the connections between geography and animal distributions, which he summarized in what became the first major modern biogeographic synthesis. Wallace traveled the island region for eight years, during which he noted the marked faunal discontinuity across what has later become known as Wallace's Line. Wallace was intrigued by the bewildering diversity and distribution of life he discovered. But even today we ask ourselves how species formed within the region and why they are not evenly distributed. Biogeography, phylogeny, dispersal, biotic interactions, and abiotic factors affect the assembly of diversity. On the basis of a decade of research on the ecology, evolution, and systematics of corvoid passerine birds, we summarize what we have learned about the biogeography and assembly of island bird diversity. Corvoid passerine birds include nearly 800 species and 2,300 named taxa and thus represent a large, well-described, and globally distributed clade. Understanding the processes influencing biodiversity in this group is certain to deepen our general understanding of ecology and evolution in the context of biogeography and faunal assembly.
Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.
Understanding variation in rates of speciation and extinction – both among lineages and through time – is critical to the testing of many hypotheses about macroevolutionary processes. Bayesian Analysis of Macroevolutionary Mixtures ( BAMM ) is a flexible Bayesian framework for inferring the number and location of shifts in macroevolutionary rate across phylogenetic trees and has been widely used in empirical studies. BAMM requires that researchers specify a prior probability distribution on the number of diversification rate shifts before conducting an analysis. The consequences of this ‘model prior’ for inference are poorly known but could potentially influence both the probability of accepting models that are more (high error rate) or less (low power) complex than the generating model.
The hierarchical Poisson process prior in BAMM reduces to a simple geometric distribution on number of rate shifts, and we use this property to increase the efficiency of model selection with Bayes factors. Using BAMM v2.5, we analysed phylogenies simulated with and without diversification heterogeneity across a broad range of prior parameterizations. We also assessed the impact of the model prior on MCMC convergence times and on diversification rate estimates.
For all simulation scenarios, model evidence (Bayes factor support) for the number of shifts is not sensitive to the choice of model prior over the wide range examined here. The best‐supported model found using BAMM rarely includes spurious shifts (<2% of all runs) when diversification models are selected using Bayes factors. BAMM was reliably able to infer the true number of diversification rate shifts across prior expectations that varied by three orders of magnitude. However, we find a strong effect of model prior on MCMC convergence properties: a flatter prior distribution (larger expected number of shifts) can dramatically increase the efficiency of the MCMC simulation.
Our results support the use of a liberal model prior in BAMM , as it reduces computation time without distorting the evidence for rate heterogeneity.
Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing NGS for the first time); 2) buy-in (i.e., getting the smallest possible amount of data from a run); and 3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 x 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: 1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and 2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5,060 UCE loci in 27 Western Scrub-Jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3,749 UCE loci containing 4,460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures we used for SNP calling. This study and other recent studies on the genomics of museums specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources. This article is protected by copyright. All rights reserved.
Todiramphus chloris is the most widely distributed of the Pacific’s ‘great speciators’. Its 50 subspecies constitute a species complex that is distributed over 16 000 km from the Red Sea to Polynesia. We present, to our knowledge, the first comprehensive molecular phylogeny of this enigmatic radiation of kingfishers. Ten Pacific Todiramphus species are embedded within the T. chloris complex, rendering it paraphyletic. Among these is a radiation of five species from the remote islands of Eastern Polynesian, as well as the widespread migratory taxon, Todiramphus sanctus. Our results offer strong support that Pacific Todiramphus, including T. chloris, underwent an extensive range expansion and diversification less than 1Ma. Multiple instances of secondary sympatry have accumulated in this group, despite its recent origin, including on Australia and oceanic islands in Palau, Vanuatu and the Solomon Islands. Significant ecomorphological and behavioural differences exist between secondarily sympatric lineages, which suggest that pre-mating isolating mechanisms were achieved rapidly during diversification. We found evidence for complex biogeographic patterns, including a novel phylogeographic break in the eastern Solomon Islands that separates a Northern Melanesian clade from Polynesian taxa. In light of our results, we discuss systematic relationships of Todiramphus and propose an updated taxonomy. This paper contributes to our understanding of avian diversification and assembly on islands, and to the systematics of a classically polytypic species complex.
The Golden Whistler (Aves: Passeriformes: Pachycephalidae) Pachycephala pectoralis sensu lato has long played a key role in the development of the theory of allopatric speciation (Mayr 1932a, b; Mayr 1942; Galbraith 1956). The P. pectoralis species complex formerly comprised 60–70 nominal subspecies and so had a distribution spanning the Indo-Pacific (Boles 2007). More recent taxonomic treatments consider the complex as multiple species-level taxa largely circumscribed by geography (Dickinson and Christidis 2014; Gill and Donsker 2014). In Australia, the endemic species P. pectoralis sensu stricto is sympatric with the closely related Mangrove Golden Whistler P. melanura. However, as the latter’s English name suggests, P. melanura is closely tied to mangroves in Australia, southeast New Guinea, and islets in the Bismarck Archipelago. Diagnostic plumage traits separating the two species are subtle: males of P. melanura have more extensively black tails and a greyer upper surface to the remiges, and females are usually yellower ventrally. All Pachycephala species, especially those in the P. pectoralis-melanura species complex, have recently become the focus of DNA sequence-based studies (Jønsson et al. 2008, 2014; Andersen et al. 2014). Data from most populations have now been analysed phylogenetically to better understand relationships and thus the history of evolution and speciation processes within and between both species. This has also been used in studies of the group’s historical biogeography to provide information as to the age of taxa and their spread across oceanic archipelagos and continents (Jønsson et al. 2014). Here we discuss the taxonomic implications of a result that has emerged consistently and independently in these studies, concerning the systematics of the southern Australian populations in south-eastern and south-western Australia, both of which have been ascribed to P. p. fuliginosa since Galbraith (1956), and we show that the name P. occidentalis Ramsay, 1878 is available for the western population and should be used for it.
The continental core of Southeast (SE) Asia, Sundaland, was assembled from Gondwana fragments by the Early Mesozoic. Continental blocks rifted from Australia in the Jurassic [South West (SW) Borneo, East Java-West Sulawesi-Sumba], and the Woyla intraoceanic arc of Sumatra, were added to Sundaland in the Cretaceous. These fragments probably included emergent areas and could have carried a terrestrial flora and fauna. Sarawak, the offshore Luconia-Dangerous Grounds areas, and Palawan include Asian continental material. These probably represent a wide accretionary zone at the Asia-Pacific boundary, which was an active continental margin until the mid Cretaceous. Subduction ceased around Sundaland in the Late Cretaceous, and from about 80 Ma most of Sundaland was emergent, physically connected to Asia, but separated by deep oceans from India and Australia. India moved rapidly north during the Late Cretaceous and Early Cenozoic but there is no evidence that it made contact with SE Asia prior to collision with Asia. One or more arc-India collisions during the Eocene may have preceded India-Asia collision. The arcs could have provided dispersal pathways from India into SE Asia before final suturing of the two continents. During the Late Cretaceous and Early Cenozoic there was no significant subduction beneath Sumatra, Java and Borneo. At about 45 Ma Australia began to move north, subduction resumed and there was widespread rifting within Sundaland. During the Paleogene east and north Borneo were largely submerged, the Makassar Straits became a wide marine barrier within Sundaland, and West Sulawesi was separated from Sundaland but included land. By the Early Miocene the proto-South China Sea had been eliminated by subduction leading to emergence of land in central Borneo, Sabah and Palawan. Australia-SE Asia collision began, eliminating the former deep ocean separating the two continents, and forming the region now known as Wallacea. The microplate or terrane concept of slicing fragments from New Guinea followed by multiple collisions in Wallacea is implausible. Neogene subduction drove extension and fragmentation of Wallacea that caused both subsidence of deep marine basins and elevation of land; topography and bathymetry changed very rapidly, especially during the Pliocene, but the detailed palaeogeography of this region remains uncertain.
Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions.
Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees.
Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral.
Contact:
warnow@illinois.edu
Supplementary information:
Supplementary data are available at Bioinformatics online.
Early studies on Melanesian mountain systems provided insights for fundamental evolutionary and ecological concepts. These island-like systems are thought to provide opportunities in the form of newly formed, competition-free niches. Here we show that a hyperdiverse radiation of freshwater arthropods originated in the emerging central New Guinea orogen, out of Australia, about 10 million years ago. Further diversification was mainly allopatric, with repeated more recent colonization of lowlands as they emerged in the form of colliding oceanic island arcs, continental fragments and the Papuan Peninsula, as well as recolonization of the central orogen. We unveil a constant and ongoing process of lineage accumulation while the carrying capacity of the island is about to be reached, suggesting that lineage diversification speed now exceeds that of landmass/new ecological opportunity formation. Therefore, the central orogeny of New Guinea acts as a motor of diversification for the entire region.
Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of less than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics.
We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere.
We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores.
These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
Although many NGS read pre-processing tools already existed, we could not find any tool or combination of tools which met our requirements in terms of flexibility, correct handling of paired-end data, and high performance. We have developed Trimmomatic as a more flexible and efficient pre-processing tool, which could correctly handle paired-end data.
The value of NGS read pre-processing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output which is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available from http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT: usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION: Manual and source code are available from http://www.usadellab.org/cms/index.php?page=trimmomatic.
Divergence time estimation using molecular sequence data relying on uncertain fossil calibrations is an unconventional statistical estimation problem. As the sequence data provide information about the distances only, estimation of absolute times and rates has to rely on information in the prior, so that the model is only semi-identifiable. In this paper, we use a combination of mathematical analysis, computer simulation, and real data analysis to examine the uncertainty in posterior time estimates when the amount of sequence data increases. The analysis extends the infinite-sites theory of Yang and Rannala, which predicts the posterior distribution of divergence times and rate when the amount of data approaches infinity. We found that the posterior credibility interval in general decreases and reaches a non-zero limit when the data size increases. However, for the node with the most precise fossil calibration (as measured by the interval width divided by the mid value), sequence data do not really make the time estimate any more precise. We propose a finite-sites theory which predicts that the square of the posterior interval width approaches its infinite-data limit at the rate 1/n, where n is the sequence length. We suggest a procedure to partition the uncertainty of posterior time estimates into that due to uncertainties in fossil calibrations and that due to sampling errors in the sequence data. We evaluate the impact of conflicting fossil calibrations on posterior time estimation and point out that narrow credibility intervals or overly precise time estimates can be produced by conflicting or erroneous fossil calibrations.
Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the 'bombycillids' (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and Bombycilloidea, although the relationships among these were unresolved. We conclude that the spotted wren-babbler represents a relict basal lineage within Passerida with no close extant relatives, and we support the already used name Elachura formosa and propose the new family name Elachuridae for this single species.
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).
Speciation is the process by which co-existing daughter species evolve from one ancestral species - e.g., humans, chimpanzees, and gorillas arising from a common ancestor around 5,000,000 years ago. However, many questions about speciation remain controversial. The Birds of Northern Melanesia provides by far the most comprehensive study yet available of a rich fauna, composed of the 195 breeding land and fresh-water bird species of the Bismarck and Solomon Archipelagoes east of New Guinea. This avifauna offers decisive advantages for understanding speciation, and includes famous examples of geographic variation discussed in textbooks of evolutionary biology. The book results from 30 years of collaboration between the evolutionary biologist Ernst Mayr and the ecologist Jared Diamond. It shows how Northern Melanesian bird distributions provide snapshots of all stages in speciation, from the earliest (widely distributed species without geographic variation) to the last (closely related, reproductively isolated species occurring sympatrically and segregating ecologically). The presentation emphasizes the wide diversity of speciation outcomes, steering a middle course between one-model-fits-all simplification and ungeneralizable species accounts. Questions illuminated include why some species are much more prone to speciate than others, why some water barriers are much more effective at promoting speciation than others, and whether hypothesized taxon cycles, faunal dominance, and legacies of Pleistocene land bridges are real. These years of study have resulted in a huge database, complete with distributions of all 195 species on 76 islands, together with their taxonomy, colonization routes, ecological attributes, abundance, and overwater dispersal. Color plates depict 88 species and allospecies, many of which have never been seen before. For students of speciation, Northern Melanesian birds now constitute a model system against which other biotas can be compared. For population biologists interested in other problems besides speciation, this rich database can now be mined for insights.
The honeyeaters are the most species-rich clade of birds east of Wallace's Line. They occupy a wide range of habitats, from desert to rainforest, and occur throughout Australia, New Guinea, and oceanic islands across Wallacea and the Pacific. Honeyeater natural history is well charac-terised, but comparative studies of this group are hampered by the lack of a well-supported phylogeny. Here, we infer the first genome-scale, genus-level phylogeny of the honeyeaters using 4397 ultraconserved elements from 57 species. We analysed the data using concatenated and species-tree approaches, and we found support for novel clades previously undetected in analyses of single-or multi-locus datasets. Despite sequencing thousands of loci, phylogenetic relationships of the New Caledonian Crow Honeyeater (Gymnomyza aubryana) remain equivocal. This study provides a new phylogenetic framework from which to study the ecology and evolution of one of Australasia's most iconic avian clades. ARTICLE HISTORY
Three isolated areas of non-rainforested open woodland habitats, often collectively termed ‘savanna’, occur in eastern New Guinea and are here termed the Trans-Fly, Central Province and Oro Province savannas. Their avifauna is mostly shared with eucalypt-dominated savannas widespread across tropical and subtropical Australia. Though the avifaunas of these New Guinean savanna regions are well-inventoried, their potential for evolutionary and ecological research has been relatively little explored. We outline the distribution and palaeoenvironmental history of these New Guinean savannas. We describe the often underappreciated floristic uniqueness and complexity of the largest bloc, which is the Trans-Fly. We discuss avian endemism and species diversity in the New Guinean savannas and we review divergence of the New Guinean populations of savanna birds from their closest relatives, usually in Australia. We review molecular phylogeographic patterns evident in New Guinea savanna birds. Several species are closest to populations or other species in north-western Australia not the geographically closer north-eastern Australia. We discuss palaeo-modelling of Pleistocene habitats that explains this. We review bird migration between Australia and the Trans-Fly. Throughout, we highlight areas for further research such as the origin of the Oro Province savannas and the origins of several distribution patterns that seem particularly puzzling.
Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographical barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographic barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.
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Australo-Pacific Petroica robins are known for their striking variability in sexual plumage coloration. Molecular studies in recent years have revised the taxonomy of species and subspecies boundaries across the southwest Pacific and New Guinea. However, these studies have not been able to resolve phylogenetic relationships within Petroica owing to limited sampling of the nuclear genome. Here, we sequence five nuclear introns across all species for which fresh tissue was available. Nuclear loci offer support for major geographic lineages that were first inferred from mtDNA. We find almost no shared nuclear alleles between currently recognized species within the New Zealand and Australian lineages, whereas the Pacific robin radiation has many shared alleles. Multilocus coalescent species trees based on nuclear loci support a sister relationship between the Australian lineage and the Pacific robin radiation—a node that is poorly supported by mtDNA. We also find discordance in support for a sister relationship between the similarly plumaged Rose Robin (P. rosea) and Pink Robin (P. rodinogaster). Our nuclear data complement previous mtDNA studies in suggesting that the phenotypically cryptic eastern and western populations of Australia's Scarlet Robin (P. boodang) are genetically distinct lineages at the early stages of divergence and speciation.
Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds. In line with previous studies, we find that one species, the little shrikethrush (C. megarhyncha) is characterized by deep divergences among populations. Delimitation results suggest that these clades represent distinct species and we consequently propose a new classification. Furthermore, our findings suggest that C. megarhyncha melanorhyncha of Biak Island does not belong in this genus, but is nested within the whistlers (Pachycephala) as sister to P. phaionota. This study represents a useful example of species delimitation when phenotypic variation is limited or poorly defined.
Molecular studies have revealed a number of cases in which traditional assessments of evolutionary relationships have been incorrect. This has implications not only for systematics and taxonomy but also for our understanding of how diversity patterns on Earth have been formed. Here, we use high-throughput sequencing technology to obtain molecular data from the holotype specimen of the elusive Eutrichomyias rowleyi, which is endemic to the Indonesian island of Sangihe. We show that E. rowleyi unexpectedly is a member of the family Lamproliidae, which dates back some 20 Million years and only include two other species, Lamprolia victoriae from Fiji and Chaetorhynchus papuensis from New Guinea. Tectonic reconstructions suggest that the Melanesian island arc, which included land masses on the northern edge of the Australian plate (present day New Guinea) stretched as a string of islands from the Philippines (including proto-Sangihe) to Fiji from 25-20 My. Consequently, our results are indicative of an ancient distribution along the Melanesian island arc followed by relictualization, which led to members of the Lamproliidae to be distributed on widely separated islands across the Indo-Pacific.
This book had its origin when, about five years ago, an ecologist (MacArthur) and a taxonomist and zoogeographer (Wilson) began a dialogue about common interests in biogeography. The ideas and the language of the two specialties seemed initially so different as to cast doubt on the usefulness of the endeavor. But we had faith in the ultimate unity of population biology, and this book is the result. Now we both call ourselves biogeographers and are unable to see any real distinction between biogeography and ecology.
Availability and implementation:
PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from https://www.github.com/faircloth-lab/phyluce/. PHYLUCE is also available as a package (https://binstar.org/faircloth-lab/phyluce) for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from http://phyluce.readthedocs.org/en/latest/ and test data are available from doi: 10.6084/m9.figshare.1284521.
Contact:
brant@faircloth-lab.org SUPPLEMENTARY INFORMATION: Supplementary Figure 1.
Major hydrocarbon discoveries have been made in eastern and westernmost New Guinea, and there is great potential for additional discoveries. Although the island is a type locality for arc-continent collision during the Cenozoic, the age, number, and plate kinematics of the events that formed the island are vigorously argued. The northern part of the island is underlain by rocks with oceanic island arc affinities, and the southern part is underlain by the Australian continental crust. Based on regional sedimentation patterns, it is argued herein that the Cenozoic tectonic history of the island involves two distinct collisional orogenic events. The first Cenozoic event, the Peninsular orogeny of Oligocene age (∼35-30 Ma), was restricted to easternmost New Guinea. Emergent uplifts that shed abundant detritus resulted from the subduction of the northeastern corner of the Australian continent beneath part of the Inner Melanesian arc. This collision uplifted the Papuan ophiolite and formed the associated mountainous uplift that was the primary source of siliciclastic sediments that largely filled the Aure trough. Between the Oligocene and Miocene, the paleogeography of the region was similar to present-day New Caledonia. The continental crust under central and western New Guinea remained a passive margin. The second event, the Central Range orogeny, began in the latest middle Miocene, when the bulldozing of Australian passive-margin strata first created emergent uplifts above a north-dipping subduction zone beneath the western part of the Outer Melanesian arc. The cessation of carbonate shelf sedimentation and widespread initiation of siliciclastic sedimentation on top of the Australian continental basement is dated at about 12 Ma. This collision emplaced the Irian ophiolite and created the present mountainous topography forming the spine of the island. Copyright ©2005. The American Association of Petroleum Geologists. All rights reserved.
The taxonomic relationships of the Australasian whistlers, or thickheads, were examined by comparing the radioiodine-labelled single-copy DNA sequences of the Golden Whistler Pachycephala pectoralis with the DNAs of fifty-five other species, representing fifty genera of oscine passerine birds (Passeres). Of the taxa examined, Pachycephala was found to be most closely related to other species of Pachycephala, to Pitohui, Colluricincla, Oreoica, Falcunculus, Rhagologus, and Daphoenositta, in that order.
The passerine family Meliphagidae (the honeyeaters) comprises 175–180 species in 40–50 genera. It is an iconic element of the Australo-Papuan avifauna and also occurs in Indonesia and on remote Pacific Ocean islands. Building on previous molecular studies that have pioneered a renewed understanding of the family's circumscription and systematics, we present an updated phylogenetic and systematics synthesis of honeyeaters derived from 112 mostly Australian, New Guinean and Wallacean species- and subspecies-rank taxa aligned across 9246 positions spanning four mitochondrial and four nuclear genes. We affirm many of the recent changes advocated to the group's genus-level systematics and offer some further refinements. The group's radiation appears to coincide broadly with the aridification of Australia in the Miocene, consistent with the time of origin of diversification of extant lineages in several other groups of Australian organisms. Most importantly, the complexity of the biogeography underlying the group's spectacular radiation, especially within Australia, is now apparent. Foremost among such examples is the robust evidence indicating that multiple, independent lineages of honeyeaters, including several monotypic genera, are endemic to the Australian arid zone, presumably having diverged and evolved within it. Also apparent and warranting further study are the phenotypic diversity among close relatives and the remarkably disjunct distributions within some clades, perhaps implying extinction of geographically intermediate lineages. Given such complexity, understanding the evolution of this radiation, which has thus far been intractable, relies on integration of molecular data with morphology, ecology and behaviour.