Coalescent Methods Research Articles

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects.

Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae)

The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. Resolving the phylogeny of the Chorthippus biguttulus species complex is important because many morphologically cryptic species occupy overlapping ranges across Eurasia and serve important ecological functions. We investigated whether multispecies coalescent analysis of 540 genes generated by transcriptome sequencing could resolve the phylogeny of the C. biguttulus complex and related Gomphocerinae species. Our divergence time estimates confirm that Gomphocerinae is a very young radiation, with an age estimated at 1.38 (2.35–0.77) mya for the C. biguttulus complex. Our estimated topology based on complete mitogenomes recovered some species as para- or polyphyletic. In contrast, the multispecies coalescent based on nuclear genes retrieved all species as monophyletic clusters, corroborating most taxonomic hypotheses. Our results underline the importance of using nuclear multispecies coalescent methods for studying young radiations and highlight the need of further taxonomic revision in Gomphocerinae grasshoppers.

StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent.

As genomic sequence data become increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent (MSC) methods address these issues. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3—a software package for efficient Bayesian inference under the MSC model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene-tree inference is parallelized, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic data sets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the data set and on the parameter, and can achieve convergence on large data sets with hundreds of genes. StarBeast3 is open-source and is easy to set up with a friendly graphical user interface. [Adaptive; Bayesian inference; BEAST 2; effective population sizes; high performance; multispecies coalescent; parallelization; phylogenetics.]

Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera

Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.

Phylogenomics and Biogeography of Populus Based on Comprehensive Sampling Reveal Deep-Level Relationships and Multiple Intercontinental Dispersals.

Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus, and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA–BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus. The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso. Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus.

Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)

AbstractSpecies of Rheum have high medicinal value, with the center of diversity in the Qinghai–Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome structure among the novel nine species along with three published species. Comparative analyses revealed that plastomes of Rheum share a relatively conserved structure. Five highly divergent regions (accD, ccsA, matK, ndhF, and ndhH) can be used as valuable molecular markers for further species delimitation and population genetic studies. Twenty‐two accessions representing 17 species were used for phylogenetic analysis, which generated a robust phylogenetic tree and revealed two major clades within Rheum. Phylogenetic results showed that glasshouse structures and cushions of Rheum are results of parallel evolution during adaptation to similar environments. Inconsistent tree topology between concatenated and coalescent methods was detected, implying that incomplete lineage sorting and hybridization may have occurred in the evolutionary history of Rheum. Divergence time estimation based on two fossil calibrations and three secondary calibrations revealed a Miocene to middle Oligocene origin of Rheum. Our study provides valuable genomic resources for the medicinally important genus Rheum, while gaining helpful insights into its systematics and evolution.

A Global Phylogenomic Study of the Thelypteridaceae

Abstract— The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, have been gained from recent phylogenetic studies; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. We sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. These were analyzed using both maximum likelihood analysis of a concatenated matrix and multi-species coalescent methods. Our phylogenomic results, informed by recently published morphological evidence, provide the foundation for a generic classification which recircumscribed 14 genera and recognized seven new genera. The 37 monophyletic genera sampled demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile and are thus inadequate for defining genera.

Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader

Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.

Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea).

The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.

Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus

AbstractGenomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution.

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]

Interspecific Gene Flow and Mitochondrial Genome Capture during the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae).

Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, Anolis opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting (ILS). Here, we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene tree, species tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene tree recovers the same relationships previously inferred for this group, which is strikingly different from the species tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model (MSCM), so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group; however, coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent, adaptive radiations. [Adaptive radiation; hybridization; introgression; multispecies network coalescent; posterior predictive simulation.].

Evolution of Potato virus X

Potato virus X (PVX) is the type potexvirus of economic significance. The pathogen is distributed worldwide, threatening solanaceous plants in particular. Based on the coat protein (CP) gene, PVX isolates are classified into two major genotypes (I and II). To gain more insights into the molecular epidemiology and evolution of PVX, recombination analyses were conducted and significant signals were detected. Bayesian coalescent method was then applied to the time-stamped entire CP sequences. According to the estimates, the global subtype I-1 went into expansion in the 20th century and was evolving at a moderate rate. Based on the CP phylogenies, a divergence scenario was proposed for PVX. Surveys of codon usage variation showed that PVX genes had additional bias independent of compositional constraint. In codon preference, PVX was both similar to and different from the three major hosts, potato (Solanum tuberosum), tobacco (Nicotiana tabacum), and tomato (S. lycopersicum). Moreover, the suppression of CpG and UpA dinucleotide frequencies was observed in PVX.

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics.

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

Theoretical and Practical Considerations when using Retroelement Insertions to Estimate Species Trees in the Anomaly Zone.

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e., local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e., clades separated by branches $>0.3$ coalescent units) with high support and identified rapid radiations (i.e., shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios. [Coalescence; incomplete lineage sorting; Laurasiatheria; Palaeognathae; parsimony; polymorphism parsimony; retroelement insertions; species trees; transposon.].

Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails.

Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 Ma, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae subfam. nov. is designated for the clade comprising Tectus, Cittarium, and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models versus concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent (MSC) model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the MSC might be necessary to resolve these and other recalcitrant nodes in the Tree of Life. [Fissurellidae; Haliotidae; likelihood mapping; multispecies coalescent; phylogenetic signal; phylogenomic conflict; site heterogeneity; Trochoidea.]

Resolving pitfalls in pit viper systematics – A multi-criteria approach to species delimitation in pit vipers (Reptilia, Viperidae, Craspedocephalus) of Peninsular India reveals cryptic diversity

Abstract Asian pit vipers belonging to the genus Craspedocephalus are a complex group of vipers, distributed in South and Southeast Asia. Their taxonomy is unresolved in many lineages across their distributional range. Here, we reassess the taxonomy and systematics of pit vipers of the genus Craspedocephalus in Peninsular India based on extensive field sampling, in particular in the Western Ghats. We build and expand on the previous findings of genetic relatedness between the peninsular Indian lineages with the Sundaic clade (C. puniceus complex) with greater evidence, based on additional taxa sequenced herein. We reconstruct the phylogeny of the group using three mitochondrial genes and delineated lineages using coalescent species delimitation methods. We then used multiple criteria including genetic divergence and separation in morphological and geographic space to designate taxonomic units. Our work revealed the presence of a South Asian radiation of the clade Craspedocephalus, with a few Sundaic members. Our study reveals the systematic relationships of four Peninsular Indian species of Craspedocephalus, including Peltopelor macrolepis and C. strigatus, sequenced here for the first time, that are classified or confirmed as members of Craspedocephalus. Hence, we place the genus Peltopelor in the synonymy of Craspedocephalus. Using our multi-criteria approach, we delimit four new cryptic evolutionary lineages within the Western Ghats escarpment of Peninsular India. These cryptic lineages belong to the C. malabaricus, C. gramineus and C. macrolepis complexes and are geographically and/or ecologically (in terms of habitat association) distinct from their sister lineages across their distributional range, while others are separated in morphological space. Our new phylogenetic tree and delimitation analysis thus reveals the presence of multiple clades with several cryptic lineages separated by geographical barriers or habitat association.

Discordance in a South African Memecylon Clade (Melastomataceae): Evidence for Reticulate Evolution

Premise of research. Evergreen forests in eastern South Africa have high biodiversity but are limited in extent and have a highly fragmented distribution. Populations of forest plants are thus geographically isolated, and fine-scale evolutionary studies of these lineages might yield important insights into the history and assembly of the forests themselves. A prior study showed that, despite their morphological diversity, three South African Memecylon taxa in Melastomataceae (Memecylon natalense, M. bachmannii, and M. australissimum) had almost identical nuclear ribosomal spacer sequences. Our study investigates phylogenetic relationships within this clade using multiple samples collected across populations and a next-generation phylogenomic approach.Methodology. We used 87 low-copy nuclear (LCN) loci to examine relationships among these taxa using both concatenated and coalescent methods. We further used LCN loci to estimate phylogenetic networks and single-nucleotide polymorphisms (SNPs) derived from LCN genes for STRUCTURE analysis of South African Memecylon populations. Finally, we employed two approaches (flow cytometry and SNPs) to infer the ploidy levels of these three taxa.Pivotal results. Our investigations showed discordance among gene trees and the species tree and low statistical support for relationships, indicating that species monophyly cannot be recovered from this phylogenomic analysis. Phylogenetic networks and population structures showed that the South African Memecylon clade may be affected by gene flow and reticulate evolution. Flow cytometry and SNP-based estimations provided evidence for polyploidy within this group.Conclusions. We found no evidence of monophyly for species within the South African Memecylon clade, which we infer to be the consequence of reticulation and recent and rapid evolution. More cytological studies and genomic data are needed to elucidate the evolutionary history of this group. Additionally, our study identifies priority populations for conservation within the South African Memecylon clade.

Understanding the convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae)†

The phylogenetic position of the capped and golden langur (CG) lineage has been ambiguous owing to the discordance between phylogenies from multiple molecular markers. Previous molecular studies have hypothesised that this discordance likely arises from either a hybridization event that took place between the Indian genus Semnopithecus and the Southeast Asian genus Trachypithecus or from incomplete lineage sorting (ILS). Distinguishing between hybridization and ILS is challenging and these processes can lead to serious difficulties in inferring phylogenies. In this study, we used genetic markers (nine nuclear and eight mitochondrial) in conjunction with coalescent based species tree approach and a test for hybridization using posterior predictive checking to better understand the evolutionary origin of the CG lineage. Both the concatenated nuclear as well as the mitochondrial dataset recovered congruent relationships where CG lineage was sister to Trachypithecus. However, nuclear species tree estimated using different multispecies coalescent methods suggested an opposite result, i.e. CG lineage was sister to Semnopithecus. Hybridization analysis strongly indicates gene flow between Semnopithecus and Trachypithecus that likely gave rise to the hybrid CG lineage. Further, the CG lineage is morphologically intermediate between Semnopithecus and Trachypithecus with respect to skull and body measurements. In light of the above evidences, we argue that the CG lineage needs to be elevated to a new genus of its own. Taxonomic and conservation implications of these results are also discussed.

A test of the centre–periphery hypothesis using population genetics in an East Asian Tertiary relict tree

AbstractAimSeveral hypotheses are available to predict change in genetic diversity at expanding peripheral ranges. However, empirical evidence to test predictions of the centre–periphery hypothesis (CPH) at contracting range limits is scarce. To address this issue, we assessed spatial patterns of genetic variation, effective population size, and contemporary and historical gene flow in a widespread, Tertiary relict tree species from subtropical China.LocationWarm‐temperate deciduous forests of subtropical China.TaxonEmmenopterys henryi (Rubiaceae)MethodsWe applied kernel density estimation to determine the centre of the species’ geographical range. Using microsatellite markers, we assessed genetic structure and diversity in 36 populations (503 individuals) sampled in the centre and periphery across the species’ range. We further examined both historical and contemporary gene flow. Finally, we applied coalescent methods to simulate population demography.ResultsIn support of CPH predictions, the highest density of E. henryi coincided with the geographical centre of the species’ distribution range, and genetic diversity significantly declined with distance from this range centre. Historical migration from the core to the edge was significantly higher than in the opposite direction, whereas contemporary migration followed an opposite pattern. Central and peripheral populations had similar levels of genetic differentiation.Main conclusionsCore‐to‐edge patterns of genetic diversity, but not genetic differentiation, were consistent with the CPH in E. henryi. Also in line with the CPH, historical (but not contemporary) migration from the core to the edge was significantly higher than in the opposite direction. Results suggest that the complex topography in subtropical China and population demographic processes may strongly influence whether CPH predictions are met in different population genetic parameters.