Multilocus Dataset Research Articles

Phylogenetic relationships and historical biogeography of silkmoths (Lepidoptera: Bombycidae) suggest an origin in Southern Gondwana

Silkmoths (Bombycidae) have a disjunct distribution predominantly in the Southern Hemisphere and Asia. Here we reconstruct the phylogenetic history of the family to test competing hypotheses on their origin and assess how vicariance and long-distance dispersal shaped their current distribution. We sequenced up to 5,074 base pairs from six loci (COI, EF1-α, wgl, CAD, GAPDH, and RpS5) to infer the historical biogeography of Bombycidae. The multilocus dataset covering 20 genera (80 %) of the family, including 17 genera (94 %) of Bombycinae and 3 genera (43 %) of Epiinae, was used to estimate phylogenetic patterns, divergence times and biogeographic reconstruction. Dating estimates extrapolated from secondary calibration sources indicate the Bombycidae stem-group originated approximately 64 Mya. The subfamilies Epiinae (South America) and Bombycinae (Australia, Asia, East Palaearctic, and Africa) were reciprocally monophyletic, diverging at c. 56 Mya (95 % credibility interval: 66–46 Mya). The ‘basal’ lineage of Bombycinae — Gastridiota + Elachyophtalma — split from the rest of Bombycinae c. 53 Mya (95 % credibility interval: 63–43 Mya). Gastridiota is a monobasic genus with a relictual distribution in subtropical forests of eastern Australia. The Oriental and African genera comprised a monophyletic group: the Oriental region was inferred to have been colonized from a long-distance dispersal event from Australia to South-East Asia c. 53 Mya or possibly later (c. 36–26 Mya); Africa was subsequently colonized by dispersal from Asia c. 16 Mya (95 % credibility interval: 21–12 Mya). Based on the strongly supported phylogenetic relationships and estimates of divergence times, we conclude that Bombycidae had its origin in the fragment of Southern Gondwana consisting of Australia, Antarctica and South America during the Paleocene. The disjunction between South America (Epiinae) and Australia (Bombycinae) is best explained by vicariance in the Eocene, whereas the disjunct distribution in Asia and Africa is best explained by more recent dispersal events.

Population genetics and phylogeography of Trachylepis sulcata (Peters, 1867) and T. ansorgii (Boulenger, 1907) in south-western Africa

ABSTRACT Ansorge’s Rock Skink Trachylepis ansorgii (Boulenger, 1907) is an Angolan taxon, the taxonomic distinctiveness and geographic distribution of which are poorly understood. It is closely related to the widespread Western Rock Skink T. sulcata (Peters, 1867) from Namibia and South Africa, but heretofore a lack of samples has prevented a comprehensive assessment of T. ansorgii in a molecular phylogenetic context. We combine new genetic sampling from south-western Angola, including topotypical material of T. ansorgii, with published sequences from South Africa and Namibia to identify population structure, phylogenetic relationships, and divergence dates within this species complex. A multi-locus dataset of three nuclear and two mitochondrial loci recovered significant population structuring with a centre of diversity in south-western Angola and northern Namibia. Mitochondrial data recovered seven clades representing distinct geographic populations, while the nuclear data supported either two or three deeper groupings. Mito-nuclear discordance was observed with respect to the geographic boundary between T. ansorgii and T. sulcata. The nuclear data support a break along the western Kunene River (the political boundary between Angola and Namibia), while the mitochondrial data support this break ∼250 km to the north in south-western Angola. A time-calibrated BEAST phylogeny found the deepest species-level divergence to have occurred in the late Miocene/early Pliocene (∼6 mya), potentially related to the formation of the Kunene River. Our results support the recognition of both taxa at the species level, and add further evidence that south-western Angola is a centre of reptile diversity.

Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group.

Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .

Rectifying a century of misidentifications: a taxonomic re-evaluation of sipo snakes (Colubridae: Chironius) on Trinidad

The island of Trinidad has several endemic reptile species that in some cases are morphologically indistinguishable, or almost so, from their mainland counterparts. In particular, many snakes from the island have not been examined thoroughly with modern scientific methods and may therefore be misidentified. At least two species of sipo snakes (Chironius carinatus, C. septentrionalis) are reported to inhabit Trinidad, both being considered species already inhabiting the mainland, though their identities are based solely on morphology. Here, we evaluate the molecular distinctiveness of these Trinidadian snakes and assess their relationships to other members of the genus. We constructed a multi-locus data set (12S rRNA, 16S rRNA, cyt b, ND4, cmos, NT3, Rag-1, Rag-2) including novel sequences and those available on GenBank to perform Bayesian and maximum likelihood phylogenetic analyses. Our phylogenetic reconstruction elucidates the identity of both Trinidad species, which have been misidentified since their discovery, and we provide a literature review of their taxonomic history. More specifically, our results suggest that the Trinidad population of Chironius carinatus is an undescribed species, that we describe herein as Chironius nigelnoriegai sp. nov., and is the sister to C. flavopictus. Our results also demonstrate that the Trinidad population previously identified as C. septentrionalis is instead the mainland species C. cochranae, a member of a clade with C. foveatus, C. laurenti, and C. multiventris. Finally, we generated a time tree and inferred that our new species separated from C. flavopictus approximately 4 million years ago in the Pliocene, a time when the island of Trinidad detached from Northern Venezuela. This work contributes to a better understanding of species diversity of Trinidad and we hope that it assists in conservation efforts towards this important endemic region. These findings support the prospect of rapid speciation on Trinidad and implies that more extensive surveys of island squamates will reveal additional cryptic diversity. http://zoobank.org/urn:lsid:zoobank.org:pub:500DB91B-62CD-4051-9831-0BEEAC64C8E2

Morphological and phylogenetic analyses reveal five new species of Porotheleaceae (Agaricales, Basidiomycota) from China.

The first occurrence of Marasmiellomycena and Pulverulina in the Chinese mycobiota are reported, M.tomentosa and P.flavoalba, two new species and M.albodescendens, a new combination, revealed by phylogenetic analyses and morphological study. These newly-recorded genera, Marasmiellomycena, which can be distinguished by their agaricoid basidiomata, dark-coloured stipe, sarcodimitic tramal structure, stipitipellis with yellow to yellowish-brown pigments and yellow-pigmented thick-walled caulocystidia and Pulverulina, which differs from other genera of Porotheleaceae by its pruinose stipe, decurrent lamellae, inamyloid basidiospores and absence of hymenial cystidia. We also formally describe three other new species of Porotheleaceae collected from Chinese temperate to subtropical zones of Fujian and Zhejiang Provinces: Clitocybulafuscostriata, Gerronemabrunneosquamulosum and Leucoinocybesubglobispora. Furthermore, we include the results of a phylogenetic analysis of Porotheleaceae, based on a multi-locus (ITS, nrLSU and rpb2) dataset. According to this analysis, Chrysomycena, Clitocybula, Delicatula, Hydropodia, Hydropus, Leucoinocybe, Marasmiellomycena, Megacollybia, Pulverulina, Trogia and Vizzinia are monophyletic. However, Gerronema is identified as polyphyletic and, additionally, Porotheleum does not form a monophyletic group either because Porotheleumparvulum and Porotheleumalbidum are "unassigned" in phylogenetic analysis. The results of our phylogenetic analyses, coupled with morphological observations, confirm recognition of these new taxa. Morphological descriptions, photographs, line drawings and comparisons with closely-related taxa are presented for the new species. A key to the 22 species belonging to nine genera of Porotheleaceae in China is also provided.

A revised phylogeny of Boletaceae using whole genome sequences

ABSTRACT The porcini mushroom family Boletaceae is a diverse, widespread group of ectomycorrhizal (ECM) mushroom-forming fungi that so far has eluded intrafamilial phylogenetic resolution based on morphology and multilocus data sets. In this study, we present a genome-wide molecular data set of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmatic Phylloboletellus chloephorus from non-ECM Argentinian subtropical forests was recovered as a new subfamily sister to the core Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and inferred vicariance associated with its disarticulation. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, establishing a foundation for future robust inferences of biogeography in the group.

Integrative methods reveal multiple drivers of diversification in rice paddy snakes

Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.

The evolution of multi-component weapons in the superfamily of leaf-footed bugs.

Sexually selected weapons, such as the antlers of deer, claws of crabs, and tusks of beaked whales, are strikingly diverse across taxa and even within groups of closely related species. Phylogenetic comparative studies have typically taken a simplified approach to investigate the evolution of weapon diversity, examining the gains and losses of entire weapons, major shifts in size or type, or changes in location. Less understood is how individual weapon components evolve and assemble into a complete weapon. We addressed this question by examining weapon evolution in the diverse, multi-component hind-leg and body weapons of leaf-footed bugs, superfamily Coreoidea (Hemiptera: Heteroptera). Male leaf-footed bugs use their morphological weapons to fight for access to mating territories. We used a large multilocus dataset comprised of ultraconserved element loci for 248 species and inferred evolutionary transitions among component states using ancestral state estimation. Our results suggest that weapons added components over time with some evidence of a cyclical evolutionary pattern-gains of components followed by losses and then gains again. Furthermore, our best estimate indicated that certain trait combinations evolved repeatedly across the phylogeny, suggesting that they function together in battle or that they are genetically correlated. This work reveals the remarkable and dynamic evolution of weapon form in the leaf-footed bugs and provides insights into weapon assembly and disassembly over evolutionary time.

Morphology and Molecular Phylogeny Reveal Five New Species of Laccaria (Hydnangiaceae, Agaricales) from Southern China.

The genus Laccaria is a type of cosmopolitan and ecologically important fungal group. Members can form ectomycorrhizal associations with numerous trees, and some species are common edible fungi in local markets. Although some new species from China are recently published, the species diversity of Laccaria is still unclear in China. In this study, some samples of Laccaria were collected from southern China, and morphological characteristics and phylogenetic analyses based on the multilocus dataset of ITS-LSU-tef1-rpb2 confirmed five new species. Laccaria miniata, L. nanlingensis and L. neovinaceoavellanea were collected from subtropical broad-leaved forests, and L. rufobrunnea and L. umbilicata were collected from subtropical mixed forests of southwest China. Full descriptions, illustrations, comparisons with similar species and phylogenetic analysis are provided.

Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes.

The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies-Hyalosphenia papilio and Hyalosphenia elegans-of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.

First Report of Anthracnose Caused by Colletotrichum asianum on Mango (Mangifera indica) in Peru.

Mangoes (Mangifera indica L.) are one of the most important export fruits in Peru and anthracnose, caused by several species in the Colletotrichum gloeosporioides species complex (CGSC), is one of their main postharvest diseases (Alvarez et al. 2020). Balsas is the major mango producing district in the Amazonas department, where farmers practice intercropping in orchards mostly of less than 5 ha (Cabezudo Cerpa 2022). In July 2021, mango fruits cv. Kent with anthracnose were detected at an incidence of 55 to 80% during postharvest in Balsas. Symptoms included sunken dark brown lesions with appearance of orange conidiomata at advanced stages of the disease. We collected two samples of infected mangoes from a farm located at 6°51'01" S, 77°59'48" W (1088 m.a.s.l.). One axenic culture (INDES-AM1) was obtained from a hyphal tip of a monosporic colony and cultivated on PDA medium at 25 °C in the dark. The growing rate of the colony was 8.1 mm.day-1. Conidia were hyaline, guttulate, unicellular and cylindrical with narrowing center, with dimensions of 15.8 to 23.5 × 4.5 to 7.6 μm (mean = 18.6 ± 0.03 × 6.0 ± 0.02 μm, SE, n = 50), consistent to the CGSC (Weir et al. 2012). Appressoria were dark brown, and ovoid to slightly irregular in shape, ranging from 5.3 to 10.1 × 4.7 to 8.3 μm (mean = 7.9 ± 0.02 × 6.0 ± 0.02 μm, SE, n = 50). Koch's postulates were fulfilled on mature mango fruits of the same cultivar and from the same district. Mangoes were washed with detergent and left to dry before inoculation. PDA-mycelial plugs of 0.5 cm wide were transferred on two different locations of two fruits, with four replicates. One location was previously wounded with five needle punctures of 3 mm depth. The inoculated fruits were maintained in a moist chamber at ambient light and temperature (18.9 ± 0.5 °C, SE). Symptoms appeared three-to-five days post inoculation (dpi), and the superficial diameter of the lesions were 8.3 ± 1.5 and 3.6 ± 2 mm with the invasive and the superficial inoculation approaches, respectively, at five dpi. Lesions were very similar to original symptoms. Macro and micromorphological characteristics of the re-isolated fungal colonies were the same as isolate INDES-AM1. Molecular identification of the pathogen was carried out following Weir et al. (2012). Total DNA was extracted using the Wizard® Genomic DNA Purification Kit (Promega Corp., Madison, Wisconsin) and the ribosomal internal transcribed spacer (ITS), and partial sequences of the chitin synthase (CHS1), actin (ACT), β-tubulin 2 (TUB2), calmodulin (CAL), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) nuclear genes were sequenced (Accession numbers: OP425395, OP440444, OP440442, OP440443, OP555062, OP555063). ITS, CHS1, ACT, TUB2, CAL, and GAPDH sequences were 98.6, 100, 100, 99.5, 100, and 99.08% identical to Colletotrichum asianum type strain ICMP 18580 sequences, respectively. Additionally, a bootstrapped maximum likelihood midpoint-rooted phylogeny with a multilocus dataset with the six sequences from reference strains of C. asianum and closely related species within the CGSC revealed that strain INDES-AM1 is C. asianum. This species has been found causing anthracnose on M. indica in at least 15 different countries in Africa, America, Asia, and Oceania (Weir et al. 2012). It was originally described from coffee and has multiple other hosts (Prihastuti et al. 2009; Lima et al. 2015). To the best of our knowledge, this is the first report of C. asianum infecting mangoes in Peru.

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes

BackgroundMitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods.ResultsWith the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80–90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes.ConclusionsThis method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.

Homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Abstract Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history. Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes. Through the use of simulation tests, we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analysing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae. Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non‐homologous sequences, such as hidden paralogs or contaminants.

Molecular Phylogeny and Morphology of Tolypocladium globosum sp. nov. Isolated from Soil in Korea

In this study, fungal strains designated as KNUF-22-14A and KNUF-22-15A were isolated from soil samples in Korea. These two strains were identified based on cultural and morphological characteristics as well as phylogenetic analyses and were found to be morphologically and phylogenetically identical. Upon their morphological comparison with closely related species, such as Tolypocladium album, T. amazonense, T. endophyticum, T. pustulatum, and T. tropicale, a difference in the size of short phialides [0.6–2.4(–9.3) × 0.8–1.4 µm] was observed. Meanwhile, these strains had larger conidia (1.2–3.0 × 1.2–3.0 µm) than T. album, T. amazonense, T. endophyticum, and T. tropicale and smaller conidia than T. pustulatum. Phylogenetic analyses using a multi-locus datasets based on ITS, LSU, and SSU showed that KNUF-22-14A and KNUF-22-15A formed a distinct cluster from previously identified Tolypocladium species. Thus, these fungal strains isolated from soil in Korea are proposed as a novel species according to their characteristics and are named Tolypocladium globosum sp. nov.

Molecular phylogeny and historical biogeography of Cyclommatus stag beetles (Coleoptera: Lucanidae): Insights into their evolution and diversification in tropical and subtropical Asia

Cyclommatus stag beetles (Coleoptera, Lucanidae) are very interesting insects, because of their striking allometry (mandibles can be longer that the whole body in large males of some species) and sexual dimorphism. They mainly inhabit tropical and subtropical forests in Asia. To date, there has been no molecular phylogenetic research on how these stag beetles evolved and diversified. In this study, we constructed the first phylogenetic relationship for Cyclommatus using multi-locus datasets. Analyses showed that Cyclommatus is monophyletic, being subdivided into two well-supported clades (A and B). The clade A includes the island species from Southeast Asia, and the clade B is formed by the continental species. The divergent time estimates showed these beetles split from the outgroup around 43.10 million years ago (Mya) in the late Eocene, divided during the late Oligocene (around 24.90 Mya) and diversified further during the early and middle Miocene (around 18.19 Mya, around 15.17 Mya). RASP analysis suggested that these beetles likely originated in the Philippine archipelago, then dispersed to the other Southeast Asian archipelagoes, Indochina Peninsula, Southeast Himalayas, and Southern China. Moreover, relatively large genetic distance and stable morphological variations signified that the two clades reach the level of inter-generic differences, i.e., the current Cyclommatus should be separated in two genera: Cyclommatus Parry, 1863 including the clade A species, and Cyclommatinus Didier, 1927 covering the clade B species. In addition, the evidence we generated indicated these beetles’ diversification was promoted probably by both long-distance dispersal and colonization, supporting an “Upstream” colonization hypothesis. Our study provides insights into the classification, genetics and evolution of stag beetles in the Oriental region.

Phylogeny of sea spiders (Arthropoda: Pycnogonida) inferred from mitochondrial genome and 18S ribosomal RNA gene sequences

The phylogeny of sea spiders has been debated for more than a century. Despite several molecular studies in the last twenty years, interfamilial relationships remain uncertain. In the present study, relationships within Pycnogonida are examined in the light of a new dataset composed of 160 mitochondrial genomes (including 152 new sequences) and 130 18S rRNA gene sequences (including 120 new sequences), from 141 sea spider morphospecies representing 26 genera and 9 families. Node congruence between mitochondrial and nuclear markers was analysed to identify the most reliable relationships. We also reanalysed a multilocus dataset previously published and showed that the high percentages of missing data make phylogenetic conclusions difficult and uncertain.Our results support the monophyly of most families currently accepted, except Callipallenidae and Nymphonidae, the monophyly of the superfamilies Ammotheoidea (Ammotheidae + Pallenopsidae), Nymphonoidea (Nymphonidae + Callipallenidae), Phoxichilidioidea (Phoxichilidiidae + Endeidae) and Colossendeoidea (Colossendeidae + Pycnogonidae + Rhynchothoracidae), and the sister-group relationship between Ammotheoidea and Phoxichilidioidea. We discuss the morphological evolution of sea spiders, identifying homoplastic characters and possible synapomorphies. We also discuss the palaeontological and phylogenetic arguments supporting either a radiation of sea spiders prior to Jurassic or a progressive diversification from Ordovician or Cambrian.

Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.

A complete genus-level phylogeny reveals the Cretaceous biogeographic diversification of the poppy family

Angiosperms, a trigger for the Cretaceous Terrestrial Revolution (KTR), underwent a rapid expansion and occupied all the environments during the Mid-Upper Cretaceous. Yet, Cretaceous biogeographic patterns and processes underlying the distribution of angiosperm diversity in the Northern Hemisphere are still poorly known. Here, we elucidated the biogeographic diversification of the angiosperm family Papaveraceae, an ancient Northern Hemisphere clade characterized by poor dispersal ability and high level of regional endemism. Based on both plastome and multi-locus datasets, we reconstructed a robust time-calibrated phylogeny that includes all currently recognized 45 genera of this family. Within the time-calibrated phylogenetic framework, we conducted 72 biogeographic analyses by testing the sensitivity of uncertainties of area delimitation, maxarea constraints, and the parameters of the model, i.e., j (describing jump-dispersal events) and w (modifying dispersal multiplier matrices), to ancestral range estimations. We also inferred ancestral habitat and ecological niches. Phylogenetic analyses strongly support Papaveraceae as monophyletic. Pteridophylloideae is strongly supported as sister to Hypecoideae-Fumarioideae. Our results indicate that the j parameter and number of predefined areas strongly affect ancestral range estimates, generating questionable ancestral ranges, whereas maxarea constraint and w parameter have no effect and improve model fit. After accounting for these uncertainties, our results indicate that Papaveraceae differentiated in Asian wet forests during the Lower Cretaceous and subsequently occupied the Asian and western North American arid and open areas. Three dispersals from Asia to western North America via the Bering land bridge occurred in the Mid-Upper Cretaceous, largely in agreement with the KTR. Habitat shift and ecological niche divergence resulted in the subsequent disjunctions between Asia and western North America. These findings suggest that the interplay of range expansion and niche divergence-driven vicariance might have shaped Cretaceous biogeographic patterns of angiosperms with Papaveraceae-like ecological requirements and dispersal abilities in the Northern Hemisphere, hence contributing to the knowledge on the geographic expansion of angiosperms during the KTR.

Towards a systematic revision of the superfamily Cyrenoidea (Bivalvia: Imparidentia): species delimitation, multi-locus phylogeny and mitochondrial phylogenomics

Cyrenoidea is a superfamily of bivalves (Bivalvia: Imparidentia) currently comprising three families (Cyrenidae, Cyrenoididae and Glauconomidae). The superfamily is widely distributed in marine, brackish and freshwater environments, with an estimated 60 or more living species. Recent phylogenetic results have confirmed the monophyly of Cyrenoidea and placement in Venerida. Nevertheless, a comprehensive phylogenetic analysis of Cyrenoidea remains elusive and the phylogeny is unresolved due to inadequate sampling in previous studies. Moreover, the taxonomy and delimitation of most species, originally based on shell morphology, have not yet been tested with molecular data. Here, we constructed three molecular datasets by sequencing three markers (<i>COI</i>+<i>16S</i> rRNA+<i>28S</i> rRNA) and complete mitogenomes for <i>Geloina coaxans</i> (Gmelin, 1791) and <i>Glauconome virens</i> (Linnaeus, 1767). <i>COI</i> barcoding clarifies the validity of <i>Geloina coaxans</i> and <i>Geloina erosa</i> that have been subject to controversy regarding synonymy. Additionally, the barcoding supports the existence of multiple cryptic species within the <i>Geloina expansa</i> complex. A multi-locus dataset (<i>COI</i>+<i>16S</i> rRNA+<i>28S</i> rRNA) provides the most comprehensive phylogeny of all eight recognised genera of Cyrenoidea to date. Phylogenetic results indicate that the currently recognised family Cyrenidae is polyphyletic. The type species <i>Geloina coaxans</i>, <i>Cyanocyclas limosa</i> (Maton, 1811) and <i>Polymesoda caroliniana</i> (Bosc, 1801) that have long been classified within the family Cyrenidae based on shell morphology, have a closer relationship with <i>Cyrenoida floridana</i> Dall, 1896 than with other Cyrenidae. Therefore we transfer the genera <i>Geloina</i>, <i>Cyanocyclas</i> and <i>Polymesoda</i> from the family Cyrenidae to the family Cyrenoididae. The mitochondrial phylogenomics further support the family-level relationships in Cyrenoidea obtained from the three-gene analyses, confirming that the newly defined Cyrenoididae is closely related to Glauconomidae as the sister group. We observed a novel gene arrangement in <i>Glauconome virens</i>, the first report on the mitogenome of the family Glauconomidae, by comparing gene arrangements. Three patterns of gene rearrangement identified in Cyrenoidea are shared by the families Glauconomidae, Cyrenoididae and Cyrenidae, suggesting that gene arrangements can be a valuable tool for phylogenetic studies.

Effects of discordance between species and gene trees on phylogenetic diversity conservation.

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying phylogenetic tree. Traditionally, phylogenetic trees were inferred from single genes and the resulting gene trees were assumed to be a valid estimate for the species tree, i.e., the "true" evolutionary history of the species under consideration. However, nowadays it is common to sequence whole genomes of hundreds or thousands of genes, and it is often the case that conflicting genealogical histories exist in different genes throughout the genome, resulting in discordance between individual gene trees and the species tree. Here, we analyze the effects of gene and species tree discordance on prioritization decisions based on the FP index. In particular, we consider the ranking order of taxa induced by (i) The FP index on a species tree, and (ii) The expected FP index across all gene tree histories associated with the species tree. On the one hand, we show that for particular tree shapes, the two rankings always coincide. On the other hand, we show that for all leaf numbers greater than or equal to five, there exist species trees for which the two rankings differ. Finally, we illustrate the variability in the rankings obtained from the FP index across different gene tree and species tree estimates for an empirical multilocus mammal data set.