Phylogenetic Placement Research Articles

Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity

BackgroundActinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340 T and ATCC 51655 T have been utilized in various studies, but their accurate species classification and description remain unresolved.ResultsTo investigate the genomic properties and taxonomic status of these strains, we employed both 16S rRNA Sanger sequencing and whole-genome sequencing using the Illumina HiSeq X Ten platform with PE151 (paired-end) sequencing. Our analyses revealed that the draft genome of Actinomyces acetigenes ATCC 49340 T was 3.27 Mbp with a 68.0% GC content, and Actinomyces stomatis ATCC 51655 T has a genome size of 3.08 Mbp with a 68.1% GC content. Multi-locus (atpA, rpoB, pgi, metG, gltA, gyrA, and core genome SNPs) sequence analysis supported the phylogenetic placement of strains ATCC 51655 T and ATCC 49340 T as independent lineages. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) analyses indicated that both strains represented novel Actinomyces species, with values below the threshold for species demarcation (70% dDDH, 95% ANI and AAI). Pangenome analysis identified 5,731 gene clusters with strains ATCC 49340 T and ATCC 51655 T possessing 1,515 and 1,518 unique gene clusters, respectively. Additionally, genomic islands (GIs) prediction uncovered 24 putative GIs in strain ATCC 49340 T and 16 in strain ATCC 51655 T, contributing to their genetic diversity and potential adaptive capabilities. Pathogenicity analysis highlighted the potential human pathogenicity risk associated with both strains, with several virulence-associated factors identified. CRISPR-Cas analysis exposed the presence of CRISPR and Cas genes in both strains, indicating these strains might evolve a robust defense mechanism against them.ConclusionThis study supports the classification of strains ATCC 49340 T and ATCC 51655 T as novel species within the Actinomyces, in which the name Actinomyces acetigenes sp. nov. (type strain ATCC 49340 T = VPI D163E-3 T = CCUG 34286 T = CCUG 35339 T) and Actinomyces stomatis sp. nov. (type strain ATCC 51655 T = PK606T = CCUG 33930 T) are proposed.

Resurrection of genus Phocanema Myers, 1959, as a genus independent from Pseudoterranova Mozgovoĭ, 1953, for nematode species (Anisakidae) parasitic in pinnipeds and cetaceans, respectively.

Species of the genus Pseudoterranova, infect kogiid cetaceans and pinnipeds. However, there is mounting molecular evidence that those from cetaceans and pinnipeds are not congeneric. Here, we provide further evidence of the non-monophyly of members of Pseudoterranova from phylogenetic analyses of the conserved nuclear LSU rDNA gene, entire ITS rDNA region and mtDNA cox2 gene, and identify morphological characters that may be used to distinguish the members of the two clades. We propose the resurrection of the genus Phocanema, with Ph. decipiens (sensu stricto) as the type species, to encompass Ph. decipiens, Ph. azarasi, Ph. bulbosa, Ph. cattani and Ph. krabbei, all parasites of pinnipeds. We propose to restrict the conception of genus Pseudoterranova, which now harbours two species infecting kogiid whales; Ps. kogiae (type species) and Ps. ceticola. Members of the genera Phocanema and Pseudoterranova differ by the shape and orientation of the lips, relative tail lengths, adult size, type of final host (pinniped vs. cetacean) and phylogenetic placement based on nuclear rDNA and mtDNA cox2 sequences.

Phylogenetic affinities of the non-cyclostome subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) confirmed by ultraconserved element data

The subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) are two small, monogeneric braconid subfamilies whose species exclusively attack lepidopteran larvae. The phylogenetic placement of Amicrocentrinae as a member of the helconoid complex of subfamilies has been supported by morphological and nuclear Sanger sequence data. The subfamilial status of Dirrhopinae on the other hand has been subject to debate, although it has been suggested as closely related to the microgastroid complex based on morphology only. Here we generated for the first time genomic ultraconserved element data for members of the above subfamilies (Amicrocentrum seyrigi van Achterberg and Dirrhope americana Muesebeck) to assess their phylogenetic affinities using exhaustive taxon sampling that includes all but one of the currently valid braconid subfamilies. Our results strongly confirm the placement of both taxa within the non-cyclostome helconoid and microgastroid complexes, respectively.

EPIK: precise and scalable evolutionary placement with informative k-mers.

Phylogenetic placement enables phylogenetic analysis of massive collections of newly sequenced DNA, when de novo tree inference is too unreliable or inefficient. Assuming that a high-quality reference tree is available, the idea is to seek the correct placement of the new sequences in that tree. Recently, alignment-free approaches to phylogenetic placement have emerged, both to circumvent the need to align the new sequences and to avoid the calculations that typically follow the alignment step. A promising approach is based on the inference of k-mers that can be potentially related to the reference sequences, also called phylo-k-mers. However, its usage is limited by the time and memory-consuming stage of reference data preprocessing and the large numbers of k-mers to consider. We suggest a filtering method for selecting informative phylo-k-mers based on mutual information, which can significantly improve the efficiency of placement, at the cost of a small loss in placement accuracy. This method is implemented in IPK, a new tool for computing phylo-k-mers that significantly outperforms the software previously available. We also present EPIK, a new software for phylogenetic placement, supporting filtered phylo-k-mer databases. Our experiments on real-world data show that EPIK is the fastest phylogenetic placement tool available, when placing hundreds of thousands and millions of queries while still providing accurate placements. IPK and EPIK are freely available at https://github.com/phylo42/IPK and https://github.com/phylo42/EPIK. Both are implemented in C++ and Python and supported on Linux and MacOS.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 5: Erysiphe (the “Microsphaera lineage” part 1)

ABSTRACT In this contribution, we offer the fifth installment of a series focusing on the phylogeny and taxonomy of powdery mildews. This paper is the second segment evaluating the genus Erysiphe. The first treatment of Erysiphe focused on phylogenetically basal species in the “Uncinula lineage.” This research presents a phylogenetic-taxonomic assessment of species that form the group previously referred to as the “Microsphaera lineage.” Given the size of the group, we split the treatment of this lineage of Erysiphe species into two parts based on their phylogenetic placement. Phylogenetic trees based on ITS+28S data are supplemented by sequences of additional markers (CAM, GADPH, GS, RPB2, and TUB). Included in the analysis of the Microsphaera lineage is the “Erysiphe aquilegiae complex” (group, clade, cluster), which encompasses sequences obtained from an assemblage of Erysiphe species with insufficient resolution in rDNA analyses. Attempts have been made to resolve this group at the species level by applying a multilocus approach. A detailed discussion of the “Erysiphe aquilegiae complex” is provided. Sequences are provided for the first time for several species, particularly North American species, such as Erysiphe aggregata, E. erineophila, E. parnassiae, and E. semitosta. Ex-type sequences for Microsphaera benzoin and M. magnusii have been retrieved. Alphitomorpha penicillata, Microsphaera vanbruntiana, and M. symphoricarpi are epitypified with ex-epitype sequences. The new species Erysiphe alnicola, E. deutziana, E. cornigena, E. lentaginis, and E. sambucina are described, the new combinations E. lauracearum, E. passiflorae, and E. sambucicola are introduced, and the new name E. santali is proposed.

Novelties and nomenclatural notes in Pabstiella (Orchidaceae) from the Brazilian Atlantic Rainforest of Bahia and Espírito Santo

Three new species of Pabstiella from Espírito Santo and Bahia in Brazil are described and illustrated, with digital plates, comparative figures, and annotations on their ecology provided. The species are compared with similar taxa, and their phylogenetic placement is hypothesized based on their morphology. In addition, five species are proposed as synonyms, P. teschiana and P. henrique-aragonii as synonyms of P. crenata, P. wanderbildtiana as synonym of P. aurantiaca, P. osculator as synonym of P. rhombilabia and P. menegattii as synonym of P. decurva. A respective taxonomic discussion is provided for each case, and a lectotype is selected for P. aurantiaca.

Candidatus Kirkpatrickella diaphorinae gen. nov., sp. nov., an uncultured endosymbiont identified in a population of Diaphorina citri from Hawaii

Diaphorina citri is the hemipteran pest and vector of a devastating bacterial pathogen of citrus worldwide. In addition to the two core bacterial endosymbionts of D. citri, Candidatus Carsonella ruddii and Candidatus Profftella armatura, the genome of a novel endosymbiont and as of yet undescribed microbe was discovered in a Hawaiian D. citri population through deep sequencing of multiple D. citri populations. Found to be closely related to the genus Asaia in the family Acetobacteraceae by 16S rRNA gene sequence analysis, it forms a sister clade along with other insect-associated 16S rRNA gene sequences from uncultured bacterium found associated with Aedes koreicus and Sogatella furcifera. Multilocus sequence analysis confirmed the phylogenetic placement sister to the Asaia clade. Despite the culturable Asaia clade being the closest phylogenetic neighbour, attempts to culture this newly identified bacterial endosymbiont were unsuccessful. On the basis of these distinct genetic differences, the novel endosymbiont is proposed to be classified into a candidate genus and species ‘Candidatus Kirkpatrickella diaphorinae’. The full genome was deposited in GenBank (accession number CP107052; prokaryotic 16S rRNA OP600170).

Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber

The correct interpretation of fossils and their reliable taxonomic placements are fundamental for understanding the evolutionary history of biodiversity. Amber inclusions often preserve more morphological information than compression fossils, but are often partially hidden or distorted, which can impede taxonomic identification. Here, we studied four new fossil species of Darwin wasps from Baltic and Dominican amber, using micro computed tomography (micro-CT) scans and 3D reconstructions to accurately interpret and increase the availability of morphological information. We then infer their taxonomic placement in a Bayesian phylogenetic analysis by combining morphological and molecular data of extant and fossil Darwin wasps and evaluate the impact and usefulness of the additional information from micro-CT scanning. The results show that although we gained significant morphological information from micro-CT scanning, especially concerning measurements and hidden dorsal and ventral structures, this did not impact subfamily-level placement for any of the four fossils. However, micro-CT scanning improved the precision of fossil placements at the genus level, which might be key in future dating and diversification analyses. Finally, we describe the four new fossil species as Rhyssa gulliveri sp. nov. in Rhyssinae, Triclistus levii sp. nov. in Metopiinae, Firkantus freddykruegeri gen. et. sp. nov. in Pimplinae and Magnocula sarcophaga gen. et sp. nov. in Phygadeuontinae. The first two species are the first known representatives of the subfamilies Rhyssinae and Metopiinae in amber.

MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies

For studies using microbiome data, the ability to robustly combine data from technically and biologically distinct microbiome studies is a crucial means of supporting more robust and clinically relevant inferences. Formidable technical challenges arise when attempting to combine data from technically diverse 16S rRNA gene variable region amplicon sequencing (16S) studies. Closed operational taxonomic units and taxonomy are criticized as being heavily dependent upon reference sets and with limited precision relative to the underlying biology. Phylogenetic placement has been demonstrated to be a promising taxonomy-free manner of harmonizing microbiome data, but it has lacked a validated count-based feature suitable for use in machine learning and association studies. Here we introduce a phylogenetic-placement-based, taxonomy-independent, compositional feature of microbiota: phylotypes. Phylotypes were predictive of clinical outcomes such as obesity or pre-term birth on technically diverse independent validation sets harmonized post hoc. Thus, phylotypes enable the rigorous cross-validation of 16S-based clinical prognostic models and associative microbiome studies.

Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement

The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64–71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the ‘repeatome’ could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I – Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.

A novel eDNA approach for rare species monitoring: Application of long-read shotgun sequencing to Lynx rufus soil pawprints

Environmental DNA (eDNA) sampling is a relatively new technique that has been employed in biodiversity surveys around the world. Environmental DNA can be an effective, non-invasive method of identifying the presence of target host species. Furthermore, advances in DNA deep sequencing technologies are enabling in-depth information to be recovered from eDNA. Here we report the development of a bobcat (Lynx rufus) species-specific probe-based qPCR assay for eDNA studies, which was validated on wild samples and those from a bobcat housed at the Jacksonville Zoo in Florida. Furthermore, we show that long-read shotgun sequencing of eDNA extracted from pawprint soil samples, using an Oxford Nanopore Technologies MinION, could successfully detect bobcat DNA, including enabling correct species level identification and phylogenetic placement within regionally distanced bobcats. This was all achieved without utilizing any DNA enrichment approaches. The long read shotgun sequencing simultaneously recovered genetic information from microbes known to be part of the bobcat microbiome, indicating that potential health-status-related microbial information can be obtained alongside wildlife eDNA. This study revealed that non-targeted (no metabarcoding or enrichment) long-read shotgun sequencing of eDNA samples can be sufficient for species identification, phylogenetic analyses, and population genetics applications. This paves the way for the rapid deployment of eDNA approaches for any species of interest, without requiring laborious development of targeted approaches, thereby increasing the ease and utility of eDNA research for endangered species conservation and management.

Ancient DNA is preserved in fish fossils from tropical lake sediments.

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.

A first genomic portrait of the deep-water azooxanthellate reef-building coral Madracis myriaster: genome size, repetitive elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Pocilloporidae

A first genomic portrait of the deep-water azooxanthellate reef-building coral Madracis myriaster: genome size, repetitive elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Pocilloporidae

A new Cretaceous orthopteran family of the Caelifera (order: Orthoptera) from Burmese amber of northern Myanmar

A new family of short horned grasshoppers, Burmecaelidae fam. nov., is described on the basis of a new species: Burmecaelinus armis fam., gen. et sp. nov. While any extant species can clearly be sorted into the Tridactylidea and Acrididea, the new fossil species presented here does not clearly match any of the two groups. The metafemora of the new family are apparently saltatorial and greatly inflated along its entire length, which is similar to extant and Mesozoic Tridactylidae and Ripipterygidae. In contrast, the compound eyes are elongated and protrude from the head dorsally; the elongated area of the pronotum does not cover the abdomen. Although the morphology of the hind legs is shared with Tridactyloidea, the shape of the head and abdomen are more similar to Tetrigoidea and Eumastacoidea. We suggest two hypotheses: (1) the new family emerged at the basis of the superfamilies Tridactyloidea and Acridoidea early in Caeliferan evolution, or alternatively (2) the new family emerged within Tridactyloidea, between the families Tridactylidae and Ripipterygidae. The new family may have emerged when these families split. The phylogenetic placement of the new family needs to be further evaluated in the future based on more specimens.

Hydnotrya qinghaiensis sp. nov. (Discinaceae, Pezizales) from Tibetan Plateau, China

Hydnotrya qinghaiensis, a new species, is described from Tibetan Plateau, China. It is characterized by the irregular globose, brownish and large ascomata. Morphologically, the new species differs from the closely related H. cerebriformis and H. variiformis by the color, size, and shape of the ascocarp and the shape of ascospores. A detailed description and comparison with closely related species are provided, and the phylogenetic placement of the new species is also discussed based on the nuclear internal transcribed spacer region (ITS).

Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.

18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae.

Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted "pan-eukaryotic" primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.

The evolution of endoparasitism and complex life cycles in parasitic platyhelminths

Within flatworms, the vast majority of parasitism is innate to Neodermata, the most derived and diversified group of the phylum Platyhelminthes.1,2 The four major lineages of Neodermata maintain various combinations of life strategies.3 They include both externally (ecto-) and internally feeding (endo-) parasites. Some lineages complete their life cycles directly by infecting a single host, whereas others succeed only through serial infections of multiple hosts of various vertebrate and invertebrate groups. Food sources and modes of digestion add further combinatorial layers to the often incompletely understood mosaic of neodermatan life histories. Their evolutionary trajectories have remained molecularly unresolved because of conflicting evolutionary inferences and a lack of genomic data.4 Here, we generated transcriptomes for nine early branching neodermatan representatives and performed detailed phylogenomic analyses to address these critical gaps. Polyopisthocotylea, mostly hematophagous ectoparasites, form a group with the mostly hematophagous but endoparasitic trematodes (Trematoda), rather than sharing a common ancestor with Monopisthocotylea, ectoparasitic epithelial feeders. Phylogenetic placement of the highly specialized endoparasitic Cestoda alters depending on the model. Regardless of this uncertainty, this study brings an unconventional perspective on the evolution of platyhelminth parasitism, rejecting a common origin for the endoparasitic lifestyle intrinsic to cestodes and trematodes. Instead, our data indicate that complex life cycles and invasion of vertebrates' gut lumen, the hallmark features of these parasites, evolved independently within Neodermata. We propose the demise of the traditionally recognized class Monogenea and the promotion of its two subclasses to the class level as Monopisthocotyla new class and Polyopisthocotyla new class.

A new species of Ecitonides Wasmann, 1894 (Coleoptera: Staphylinidae: Paederinae) from Peru and phylogenetic placement of the genus based on molecular data.

Ecitonides constanceae sp. nov., a new species of the myrmecophilous genus Ecitonides Wasmann, 1894, which is associated with army ants (Hymenoptera: Formicidae: Ecitoninae), is described from Peru. The holotype, which is the only known specimen, was collected at light at Los Amigos Biological Station, Madre de Dios department, Peru. The army ant host species is unknown. The new species is distinguished from congeners and an updated key of the species, as well as a checklist of Ecitonides and their associated host ants are provided. Based on the holotype we non-destructively extracted DNA and sequenced two genes which were incorportated into an existing molecular phylogenetic dataset and analysed using Bayesian Inference. Ecitonides is recovered as sister to recently described thermitophilous genus Ruptor ya et al. 2022 and placed in the so-called Medonina and allied taxa clade. Beyond Bayesian Inference phylogenetic analysis and their associated nodal support methods, we also explored the position of the Ecitonides within the posterior sample of trees produced in the Bayesian analyses, which further supported its placement.

Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse

Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater’s Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater’s Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genomic components associated with the Z-chromosome influence the phenotype and thereby impact species limits among prairie grouse taxa despite ongoing contemporary gene flow.