Nuclear Gene Sequences Research Articles

Multiple origin of flightlessness in Phaneropterinae bushcrickets and redefinition of the tribus Odonturini (Orthoptera: Tettigonioidea: Phaneropteridae)

The possession of wings and ability to fly are a unifying character of higher insects, but secondary loss of wings is widespread. Within the bushcrickets, the subfamily Phaneropterinae (Orthoptera: Tettigonioidea) comprises more than 2000 predominantly long-winged species in the tropics. However, the roughly 300 European representatives are mainly short-winged. The systematics of these radiations have been unclear, leading to their unreliable formal treatment, which has hindered analysis of the evolutionary patterns of flight loss. A molecular phylogeny is presented for 42 short-winged species and members of all European long-winged genera based on the combined data from three nuclear gene sequences (18S, H3, ITS2). We found four phylogenetic lineages: (i) the first included the short-wing species of the genus Odontura; (ii) a further branch is represented by the South-American short-winged Cohnia andeana; (iii) an assemblage of long-wing taxa with a deep branching pattern includes the members of the tribes Acrometopini, Ducetiini, Phaneropterini, and Tylopsidini; (iv) a large group contained all short-winged taxa of the tribe Barbitistini. Phaneropterinae flightlessness originated twice in the Western Palaearctic, with a number of mainly allo- and parapatrically distributed species of the Barbistini in Southeastern Europe, and the Middle East and a limited number of Odontura species in Northern Africa and Southwestern Europe. Both short-winged lineages are well separated, which makes it necessary to restrict the tribe Odonturini to the West-Palaearctic genus Odontura. Other flightless genera previously included in the Odonturini are placed as incertae sedis until their phylogenetic position can be established.

Zenkevitchiidae fam. nov. (Crustacea: Gammaroidea), with description of new subterranean amphipods from extremely deep cave habitats

ABSTRACTPrevious phylogenetic analysis based on combined mitochondrial and nuclear gene sequences detected paraphyly of the Typhlogammaridae. To test this hypothesis a portion of large subunit (LSU-rDNA) gene sequences were obtained for typhlogammarid species from Caucasus. The Bayesian approach to LSU-rDNA sequences provided evidence for an independent origin of the Dinaric and Caucasus ‘typhlogammarid’ clades. A new family, Zenkevitchiidae fam. nov., is proposed to reconcile the observed phylogeny with the concept of monophyly. Using light microscopy, two mouthpart morphotypes of the Zenkevitchiidae fam. nov. species with quite different setae are identified. Taking into account these two morphotypes, a new classification is proposed – Adaugammarus revazi comb. nov., and Adaugammarus sandroruffoi comb. nov. Additionally, two new stygobiont zenkevitchiid amphipod species – Adaugammarus kasiani sp. nov. and Kruberia relicta sp. nov. – are described from Krubera Cave in Abkhazia. A distribution map and an identification key for the Zenkevitchiidae fam. nov. species of Transcaucasia are provided.http://zoobank.org/urn:lsid:zoobank.org:pub:90177B0C-BED0-4601-8CFC-3F774B22065C

Investigating the genetic diversity of Echinococcus granulosus sensu stricto with new microsatellites.

Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the predominance or even the exclusive presence of E. granulosus sensu stricto (s.s.) among E. granulosus species in many areas, the genetic diversity needs to be further investigated at the species level to better understand the inter- and intra-focus epidemiological features. Short sequences of mitochondrial or nuclear genes generally lack or have limited discriminatory power, hindering the detection of polymorphisms to reflect geographically based peculiarities and/or any history of infection. A high discriminatory power can only be reached by sequencing complete or near complete mitogenomes or relatively long nuclear sequences, which is time-consuming and onerous. To overcome this issue, a systematic research for single-locus microsatellites was performed on the nuclear genome of E. granulosus s.s. in order to investigate its intra-species genetic diversity. Two microsatellites, EgSca6 and EgSca11, were selected and characterized. The test of a panel of 75 cystic echinococcosis samples revealed a very high discrimination index of 0.824 for EgSca6, 0.987 for EgSca11, and 0.994 when multiplexing both microsatellites. Testing cystic echinococcosis samples from both liver and lungs in five sheep revealed that these two microsatellites appear to be of particular interest for investigating genetic diversity at the intra-individual host level. As this method has many advantages compared to classical sequencing, the availability of other targets means that it is potentially possible to constitute a panel facilitating large-scale molecular epidemiology studies for E. granulosus s.l.

An effective method for identification of three mussel species and their hybrids based on SNPs

We described here the successful identification of three economic aquaculture mussel species in China and their hybrids by high resolution melting curve analysis (HRM) of single nucleotide polymorphisms (SNPs). The nuclear 18S ribosomal RNA gene sequences from Mytilus edulis, Mytilus coruscus, and Perna viridis were aligned and amplified. In total, 8 SNP sites were detected from the 79-bp amplicon. A total of 90 samples from the three mussel species were clearly separated, hybrids from M. edulis and M. coruscus could also be clearly identified. The melting profiles from HRM analysis were found to be distinct across the species tested. This new identification method will be a useful tool for discrimination of the three commercially important mussel species and their hybrids.

Genetic Divergence of Mussels (Mollusca, Mytilidae) Based on the 28S rRNA, 18S rRNA, and H3 Nuclear Gene Sequences

On the basis of nucleotide sequences of three nuclear genes and using molecular phylogenetic and evolutionary genetic approaches, the phylogeny of the main representatives of one of the largest taxa of bivalve mollusks, the family Mytilidae, was studied, and its system and taxonomy were refined. A phylogenetic system for the family Mytilidae and closely relative taxa of the order Mytilida, which currently has no consensus among specialists on the basis of traditional characters, is presented. Using nucleotide sequences of the 28S rRNA, 18S pRNA, and histone H3 genes, this consensus was established by the study of Mytilidae. Some concerns of mussel systematics were resolved; in particular, the monophyly of the family Mytilidae Rafinesque, 1815 was established with the strongest support for the subfamily Mytilinae Rafinesque, 1815. The data obtained disprove Distel’s conclusion on polyphyly of the subfamily Mytilinae Rafinesque, 1815. Isolation of the taxa in the rank of the Modiolinae G. Termier & H. Termier, 1950 and Bathymodiolinae Kenk & Wilson, 1985 subfamilies in the family Mytilidae and also the family Septiferidae Scarlato et Starobogatov, 1979 was confirmed, although the rank of the later taxon is not universally recognized and it remains to be clarified in an additional study.

Orthonectids Are Highly Degenerate Annelid Worms

The animal groups of Orthonectida and Dicyemida are tiny, extremely simple, vermiform endoparasites of various marine animals and have been linked in the Mesozoa (Figure1). The Orthonectida (Figures 1A and 1B) have a few hundred cells, including a nervous system of just ten cells [2], and the Dicyemida (Figure1C) are even simpler, with ∼40 cells [3]. They are classic "Problematica" [4]-the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) [5] and implies that their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria [6-9], which means that they derive from a more complex ancestor. Their precise affinities remain uncertain, however, and it is disputed whether they even constitute a clade. Ascertaining their affinities is complicated by the very fast evolution observed in their genes, potentially leading to the common systematic error of long-branch attraction (LBA) [10]. Here, we use mitochondrial and nuclear gene sequence data andshow that both dicyemids and orthonectids aremembers of the Lophotrochozoa. Carefully addressing the effects of unequal rates of evolution, we show that the Mesozoa is polyphyletic. While theprecise position of dicyemids remains unresolved within Lophotrochozoa, we identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body-plan simplification in the animal kingdom; ourfinding makes sense of an annelid-like cuticle in orthonectids [2] and suggests that the circular muscle cells repeated along their body [11] may be segmental in origin.

Morphological and molecular identification of a new species of Perenniporia (Polyporales, Basidiomycota) in North America

A new poroid wood-inhabiting fungal species, Perenniporia bostonensis sp. nov., is proposed based on morphological and molecular characters. The species is characterized by resupinate, cream to buff pore surface; a dimitic hyphal system with skeletal hyphae strongly dextrinoid, unbranched, interwoven and a distinct wide lumen; ovoid to broad ellipsoid, non-truncate, hyaline, distinct thick-walled, smooth, dextrinoid basidiospores, 3.5–4.5 × 3–4 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on molecular data of ITS+nLSU sequences showed that P. bostonensis recognized in Perenniporia sensu stricto. The new species formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and was closely related to P. bannaensis and P. koreana. Both morphological and molecular characters confirmed the placement of the new species in Perenniporia.

Morphological and molecular identification of a new species of Perenniporia (Polyporales, Basidiomycota) in North America

A new poroid wood-inhabiting fungal species, Perenniporia bostonensis sp. nov., is proposed based on morphological and molecular characters. The species is characterized by resupinate, cream to buff pore surface; a dimitic hyphal system with skeletal hyphae strongly dextrinoid, unbranched, interwoven and a distinct wide lumen; ovoid to broad ellipsoid, non-truncate, hyaline, distinct thick-walled, smooth, dextrinoid basidiospores, 3.5–4.5 × 3–4 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on molecular data of ITS+nLSU sequences showed that P. bostonensis recognized in Perenniporia sensu stricto. The new species formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and was closely related to P. bannaensis and P. koreana. Both morphological and molecular characters confirmed the placement of the new species in Perenniporia.

Biogeography and species delimitation of the rheophilic suckermouth catfish genus Pseudolithoxus (Siluriformes: Loricariidae), with the description of a new species from the Brazilian Amazon

The rapids-dwelling suckermouth catfish genus Pseudolithoxus was previously only known from the Guiana-Shield-draining Orinoco and Casiquiare river systems of Colombia and Venezuela, but new records have expanded this range considerably further into the Amazon basin of Brazil, and include occurrences from rivers draining the northern Brazilian Shield. These highly disjunct records are now placed in an evolutionary and phylogeographic context using a dated species tree constructed from mitochondrial (Cytb) and nuclear (RAG1) gene sequence data. Due to mito-nuclear discordance, we also delimit the putative species using statistical coalescent models and a range of additional metrics. We infer that at least two species of Pseudolithoxus are present in the Amazon basin: P. nicoi, previously only recorded from the río Casiquiare, but now also reported from the upper rio Negro, and a new species, which we describe herein from south-draining Guiana Shield and north-draining Brazilian Shield. Our data reject a simple model of Miocene vicariance in the group following uplift of the Uaupés Arch separating the Orinoco and Amazon systems, and instead suggest more complex dispersal scenarios through palaeo-connections in the Pliocene and also via the contemporary rio Negro and rio Madeira in the late Pleistocene.www.zoobank.org/urn:lsid:zoobank.org:pub:46A6BEC1-1A1B-4244-80-A6-FD9CF8DA0384.

Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)

Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of ‘taxonomics’. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.

Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora)

Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

Partnerships Between Ambrosia Beetles and Fungi: Lineage-Specific Promiscuity Among Vectors of the Laurel Wilt Pathogen, Raffaelea lauricola.

Nutritional mutualisms that ambrosia beetles have with fungi are poorly understood. Although these interactions were initially thought to be specific associations with a primary symbiont, there is increasing evidence that some of these fungi are associated with, and move among, multiple beetle partners. We examined culturable fungi recovered from mycangia of ambrosia beetles associated with trees of Persea humilis (silk bay, one site) and P. americana (avocado, six commercial orchards) that were affected by laurel wilt, an invasive disease caused by a symbiont, Raffaelea lauricola, of an Asian ambrosia beetle, Xyleborus glabratus. Fungi were isolated from 20 adult females of X. glabratus from silk bay and 70 each of Xyleborus affinis, Xyleborus bispinatus, Xyleborus volvulus, Xyleborinus saxesenii, and Xylosandrus crassiusculus from avocado. With partial sequences of ribosomal (LSU and SSU) and nuclear (β-tubulin) genes, one to several operational taxonomic units (OTUs) of fungi were identified in assayed individuals. Distinct populations of fungi were recovered from each of the examined beetle species. Raffaelea lauricola was present in all beetles except X. saxesenii and X. crassiusculus, and Raffaelea spp. predominated in Xyleborus spp. Raffaelea arxii, R. subalba, and R. subfusca were present in more than a single species of Xyleborus, and R. arxii was the most abundant symbiont in both X. affinis and X. volvulus. Raffaelea aguacate was detected for the first time in an ambrosia beetle (X. bispinatus). Yeasts (Ascomycota, Saccharomycotina) were found consistently in the mycangia of the examined beetles, and distinct, putatively co-adapted populations of these fungi were associated with each beetle species. Greater understandings are needed for how mycangia in ambrosia beetles interact with fungi, including yeasts which play currently underresearched roles in these insects.

Diversity and evolution of rice progenitors in Australia.

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.

Genetic Structure of Dytiscus sharpi in North and South Hokuriku in Japan Inferred from Mitochondrial and Nuclear Gene Sequence

Dytiscus sharpi is a critically endangered diving beetle endemic to Japan that is distributed in five distant areas today. Information on the population genetics of this species is crucial for its conservation. We investigated the genetic differentiation and divergence of the D. sharpi in seven populations in North and South Hokuriku on the Sea of Japan side, using mitochondrial cytochrome oxidase subunit I (COI) and nuclear Histone 3 and 28S rRNA gene sequences. Although the nuclear markers showed little geographic genetic differentiation, nine COI haplotypes were identified from 31 individuals, and these haplotypes were divided into two distinct networks A and B. The network A consisted of a single haplotype, and network B consisted of eight haplotypes. The populations in North Hokuriku possessed the haplotypes of both networks, whereas those in South Hokuriku possessed only the haplotypes of network B. The genetic diversity was relatively high in South and North Hokuriku. However, populations in South Hokuriku showed low genetic diversity and the isolation-by-distance pattern was observed among the populations, suggesting a restricted gene flow. Phylogenetic analysis including the data from a previous study revealed that the network A was closely related to a haplotype from Kanto, which is on the Pacific side. These results suggested that in the past this species was distributed widely across the Hokuriku area and the fragmentation of its distribution areas is a recent event. These results will contribute to strategies for the preservation of the current genetic diversity of D. sharpi.

Diagnostic odyssey of patients with mitochondrial disease: Results of a survey.

ObjectiveTo document the complex “diagnostic odyssey” of patients with mitochondrial disease.MethodsWe analyzed data from 210 Rare Diseases Clinical Research Network Contact Registry participants who were patients with a biochemical deficiency or self-reported diagnosis of mitochondrial disease, or their caregivers.ResultsParticipants saw an average of 8.19 clinicians (SD 8.0, median 5). The first clinician consulted about symptoms was typically a primary care physician (56.7%), although 35.2% of participants initially sought a specialist. Of note, 55.2% of participants received their diagnosis from a neurologist, 18.2% from a clinical geneticist, and 11.8% from a metabolic disease specialist. A majority of the participants (54.6%) received 1 or more nonmitochondrial diagnoses before their final mitochondrial diagnosis. In their pursuit of a diagnosis, 84.8% of participants received blood tests, 71% a muscle biopsy, 60.5% MRI, and 38.6% urine organic acids. In addition, 39.5% of the participants underwent mitochondrial DNA sequencing, 19% sequencing of nuclear gene(s), and 11.4% whole-exome sequencing.ConclusionsThe diagnostic odyssey of patients with mitochondrial disease is complex and burdensome. It features multiple consultations and tests, and, often, conflicting diagnoses. These reflect disease variety, diagnostic uncertainty, and clinician unfamiliarity. The current survey provides an important benchmark. Its replication at appropriate intervals will assist in tracking changes that may accompany increased popularity of exome testing, more rigorous diagnostic criteria, increased patient reported outcome activity, and trials for promising therapies.

Novel Collophorina and Coniochaeta species from Euphorbia polycaulis, an endemic plant in Iran

During a study on the biodiversity of yeasts and yeast-like ascomycetes from wild plants in Iran, four strains of yeast-like filamentous fungi were isolated from a healthy plant of Euphorbia polycaulis in the Qom Province, Iran (IR. of). All four strains formed small hyaline one-celled conidia from integrated conidiogenous cells directly on hyphae and sometimes on discrete phialides, as well as by microcyclic conidiation. Two strains additionally produced conidia in conidiomata that open by rupture. The internal transcribed spacer (ITS) sequences suggested the placement of these strains in the genera Collophorina (Leotiomycetes) and Coniochaeta (Sordariomycetes), respectively. Blast search results on NCBI GenBank and phylogenetic analyses of ITS, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the translation elongation factor 1α (EF-1α) sequences, and the nuclear large subunit ribosomal gene (LSU), partial actin (ACT), and β-tubulin (TUB) sequences, respectively, revealed the isolates to belong to three new species, that are described here as Collophorina euphorbiae, Coniochaeta iranica, and C. euphorbiae. All three species are characterised by morphological, physiological, and molecular data.

Hidden genetic history of the Japanese sand dollar Peronella (Echinoidea: Laganidae) revealed by nuclear intron sequences

The marine environment around Japan experienced significant changes during the Cenozoic Era. In this study, we report findings suggesting that this dynamic history left behind traces in the genome of the Japanese sand dollar species Peronella japonica and P. rubra. Although mitochondrial Cytochrome C Oxidase I sequences did not indicate fragmentation of the current local populations of P. japonica around Japan, two different types of intron sequence were found in the Alx1 locus. We inferred that past fragmentation of the populations account for the presence of two types of nuclear sequences as alleles in the Alx1 intron of P. japonica. It is likely that the split populations have intermixed in recent times; hence, we did not detect polymorphisms in the sequences reflecting the current localization of the species. In addition, we found two allelic sequences of theAlx1 intron in the sister species P. rubra. The divergence times of the two types of Alx1 intron sequences were estimated at approximately 14.9 and 4.0 million years ago for P. japonica and P. rubra, respectively. Our study indicates that information from the intron sequences of nuclear genes can enhance our understanding of past genetic events in organisms.

On geographic barriers and Pleistocene glaciations: Tracing the diversification of the Russet-crowned Warbler (Myiothlypis coronata) along the Andes.

We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M. orientalis, M. c. chapmani), and central Peru and Bolivia (M. c. coronata). We found further population structure within M. c. regulus and M. c. coronata, and population structure and complexity of plumage variation within the Ecuador-northern Peru lineage. Time-calibrated trees estimated that most intraspecific variation originated during the Pleistocene; however, this pattern may not be attributed to an increase in diversification rate during that period. We discuss these results in the context of the importance of geographic-ecological barriers in promoting lineage diversification along the Andes and put forward a preliminary taxonomic proposal for major lineages identified in this study.

×Lindsaeosoria flynnii(Lindsaeaceae), Another Confirmed Example of Deep Hybridization Among the Ferns

The origin of ×Lindsaeosoria flynnii as an intergeneric hybrid between Lindsaea ensifolia and Odontosoria chinensis is here confirmed by molecular analysis of plastid data and Illumina high-throughput sequencing of the low-copy nuclear LEAFY gene. Plastid DNA grouped the hybrid together with Lindsaea ensifolia, suggesting that it is the maternal progenitor, while the presence of distinct LEAFY alleles confirmed the hybrid origin. Together with ×Cystocarpium this is confirmed example of deep hybridization event between fern lineages that were separated in the early Cenozoic or late Mesozoic.

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus.

Untapped information about allele diversity within populations and individuals (i.e., heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allele data across unlinked loci, and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target-enriched Illumina sequencing libraries. We performed supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences: a consensus method based on de novo sequence assembly, the use of ambiguity characters, and a novel method for incorporating read information to phase alleles. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves phylogenetic resolution or decreases topological uncertainty. We show here that it is possible to infer phased alleles from target-enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency. We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. In our data set, the impact of allele phasing on phylogeny is minimal compared to the impact of using phylogenetic reconstruction methods that account for gene tree incongruence.