Wiley: Zoologica Scripta: Table of Contents

Molecular Phylogeny of Tiny Land Snails From the Family Punctidae (Stylommatopohora, Punctoidea) in Australia

Isabel T. Hyman, Guoyi Zhang, Frank Köhler — Mon, 25 May 2026 06:55:19 -0700

ABSTRACT

The Punctidae is a group of small to minute land snails with their centre of diversity in Australia and New Zealand. We present a comprehensive molecular phylogeny of Australian punctids based on mitochondrial (COI, 16S) and nuclear (ELAVI8, ITS2) markers, including 27 of the 32 mainland and Tasmanian species, as well as representative samples from Lord Howe Island, Norfolk Island, Macquarie Island and New Zealand. Measurements of shell dimensions of all sequenced specimens were analysed using the Kruskal–Wallis rank-sum test to assess morphological support for branching patterns. The Australian punctids comprise a large unresolved radiation made up mostly of mainland species that diverged around 5.5 Ma, with more basal groups comprising taxa from Tasmania, New Zealand, Macquarie Island, Lord Howe Island and Norfolk Island. To better reflect the pattern of rapid diversification of punctids on the Australian mainland, and supported by morphological data, we treat the genera Gratilaoma, Iotula, Laomavix, Miselaoma, Pseudiotula, Tescilaoma, Trocholaoma and Westralaoma as junior synonyms of Paralaoma. We demonstrate that Pasmaditta jungermanniae, Pedicamista sp. ‘Bull Hill’ and Trocholaoma spiceri are part of Cystopeltidae rather than Punctidae, and that the Norfolk Island charopids Norfolcioconcha, Penescosta, Cryptocharopa and Frustropa belong to Punctidae. Based on molecular data and examination of types, we treat Paralaoma annabelli as a junior synonym of Paralaoma mucoides, Westralaoma experta as a junior synonym of Paralaoma morti, and Westralaoma expicta as a junior synonym of Paralaoma servilis.

Chromosome‐Level Genome Assembly of Otocolobus manul Provides Insights Into High‐Altitude Adaptation and Evolutionary Traits

Shuo Feng, Xin Tang, Qiang Gao, Xin‐Zhang Qi, De‐Ling Qi — Mon, 25 May 2026 00:00:00 -0700

ABSTRACT

The Otocolobus manul, a small felid endemic to the high-altitude Qinghai-Tibet Plateau, lacks a high-quality chromosome-level genome, hindering study of its evolutionary adaptations. This study aimed to construct such a genome and investigate its genetic basis for high-altitude adaptation. We generated a de novo chromosome-scale assembly using an integrated approach of PacBio HiFi long-reads, Illumina short-reads, and Hi-C scaffolding. The resulting 2.55 Gb genome was anchored to 19 chromosomes (contig N50 = 96.32 Mb) and contained 22,699 protein-coding genes. Comparative genomic analysis across felids revealed 13 expanded gene families in O. manul, functionally enriched in processes like glycolysis/gluconeogenesis and the HIF-1 signalling pathway. Phylogenetic analysis placed O. manul as sister to Prionailurus, with an estimated divergence time of 6.10–7.04 million years ago, and identified positive selection signals linked to adaptation. Furthermore, we found that the nuclear genome supports a sister relationship between O. manul and Prionailurus (they are closely related species), while the mitochondrial genome suggests a closer relationship with Felis. This significant mito-nuclear phylogenetic discordance is primarily attributed to incomplete lineage sorting (ILS). This de novo chromosome-level genome assembly of O. manul provides a crucial resource for evolutionary and conservation studies. The findings specifically highlight significant genetic enrichments in hypoxia-responsive pathways, suggesting its molecular adaptation to the extreme plateau environment.

Last Tile Added to a Mosaic: Phylogenetic Placement of Enigmatic Freshwater Fish Leucalburnus satunini (Cypriniformes: Leuciscidae) Uncovered

Jasna Vukić, Eleni A. Charmpila, Cüneyt Kaya, Radek Šanda — Thu, 21 May 2026 06:39:02 -0700

ABSTRACT

Subfamily Leuciscinae, the largest freshwater fish group of the western Palearctic region, has been widely studied, including the phylogenetic relationships between its species and genera. However, until now, one genus completely escaped attention in this regard. Even though several works hypothesised about its evolutionary relationships based on its scarce morphological data, they did not succeed in resolving this puzzle, and their assumptions were often contradictory. Our study aimed to bring insight into the phylogenetic origin and relationships of the enigmatic Caucasian genus Leucalburnus based on the most taxon-dense, multilocus molecular analyses of the subfamily Leuciscinae so far. Moreover, a time-calibrated phylogenetic reconstruction was performed in order to put the emergence of the Leucalburnus lineage in a timeframe. In our analyses, Leucalburnus was consistently recovered as a member of the Alburnus clade, which further comprises Alburnus, Leucaspius and Anaecypris, adding thus one more genus to the clade and providing more evidence of non-monophyly of the genus Alburnus.

Genome‐Wide SNP Variation as a Test for Mitochondrial Phylogeography and Karyotypic Groups in the Common Shrew (Soricidae, Mammalia)

Wed, 20 May 2026 08:20:35 -0700

ABSTRACT

Nuclear variation and phylogeography of the chromosomally highly polymorphic common shrew (Sorex araneus) represent a subject of considerable interest for understanding microevolutionary processes in wide-ranging mammals. In the present study, we addressed this issue using SNP data generated via the ddRADseq approach and based on extensive geographic sampling. Our results are consistent with the hypothesis of a recent range expansion from a refugium located in the Balkan-Danubian region, followed by subsequent colonization of Eastern Europe and, later, Siberia. This scenario had previously been proposed on the basis of mitochondrial DNA data. On the contrary, genetic relatedness of shrews from southern Karelia and central Siberia, as suggested previously from mtDNA variation, is not supported by our SNP dataset. Nuclear data reveal substantial gene flow across the boundaries between chromosomal races and racial groups.

Molecular Evidence for the Placement of Microcerberidae (Crustacea: Isopoda) Within the Suborder Asellota and Invalidity of the Suborder Microcerberidea

Sat, 16 May 2026 03:50:14 -0700

ABSTRACT

Since their discovery, the question of the phylogenetic position of Microcerberidae within Isopoda has been widely debated. Initially perceived as close relatives of the Anthuridae, the debate has shifted towards considering them either as a sister group of Asellota or positioned within the Asellota in their own right. In this study, we used sequence data for eight slow-evolving nuclear genes in 37 isopod taxa to test for the hypothesis that Microcerberidae were Asellota and, as such, should not be regarded as an independent suborder within the Isopoda. We also evaluated the earlier hypothesis of a sister relationship between the Anthuridae and Microcerberidae. Altogether, our results provide strong evidence in favour of a clade including the Microcerberidae and the Aselloidea, which supports the invalidation of the suborder Microcerberidea.

Integrative Taxonomic Reappraisal and Molecular Phylogeny of Freshwater Mussels of the Genus Lanceolaria (Bivalvia: Unionidae), With Description of Two New Species

Sat, 02 May 2026 01:04:41 -0700

ABSTRACT

Effective species conservation requires accurate identification of target taxa; however, the large intraspecific variation and strong phenotypic plasticity of shell morphology in freshwater mussels (Bivalvia: Unionidae) exacerbate taxonomic uncertainties, thereby complicating species delineation. Based on extensive geographic sampling, we conducted an integrative taxonomic revision and phylogenetic reconstruction of the freshwater mussel genus Lanceolaria by integrating shell morphology, geometric morphometrics, sequence data from multiple gene loci (COI, 16S rRNA, 18S rRNA and 28S rRNA) and mitogenome datasets. Molecular species delimitation methods and Fourier morphometric analysis confirmed two new species: Lanceolaria danzhouensis sp. nov., distributed in southern China and Vietnam and closely related to Lanceolaria grayii; and Lanceolaria helianthoides sp. nov., from Guangdong Province, China, which is closely related to Lanceolaria lanceolata. Additionally, we recognized Lanceolaria cylindrica syn. nov., Lanceolaria eucylindrica syn. nov. and Lanceolaria yueyingae syn. nov. as junior synonyms of Lanceolaria grayii, and the species exhibited extremely strong environmental adaptability and phenotypic plasticity. We first sequenced the mitochondrial genomes of five species within the genus. Based on multilocus and mitogenomic phylogenetic analyses, our results elucidated intrageneric relationships and revealed three major clades. Overall, we clarified the classification of the genus Lanceolaria, resolved long-standing taxonomic disputes, evaluated its species diversity and provided a reliable phylogenetic and taxonomic framework for this genus.

What You Can See From here: A Critical Role of Integrative Approach and Sample Size in Defining Species Boundaries for Trans‐Arctic Nudibranchs (Gastropoda: Heterobranchia)

Fri, 01 May 2026 05:24:27 -0700

ABSTRACT

Recent integrative taxonomic revisions of the amphiboreal nudibranch Diaphoreolis viridis (Forbes, 1840) suggest that it represents a complex of cryptic or pseudocryptic species. However, species delimitation within trans-Arctic taxa remains challenging due to the reliance on potentially variable morphological traits (such as coloration) and the limitations of using mtDNA data alone. Therefore, the taxonomic status of several North Pacific populations traditionally attributed to the Diaphoreolis viridis complex (Diaphoreolis midori (Martynov, Sanamyan & Korshunova, 2015), Diaphoreolis viridis emeraldi Korshunova, Fletcher, Bakken & Martynov, 2023, and the nominal form) requires rigorous re-evaluation using integrative approaches. The aim of this study is to clarify the identity of chromatic variants of D. viridis across its broad Pacific distribution and to assess the genetic connectivity of its distant populations. By combining detailed morphological examination with mtDNA genotyping and sequencing of nuclear ribosomal markers across a wide geographic range of the complex, this study provides a robust assessment of species boundaries within Diaphoreolis viridis and contributes to a broader understanding of the challenges and solutions in trans-Arctic nudibranch taxonomy. The phylogeographic analysis included a TCS-based network analysis, an analysis of molecular variance (AMOVA) and divergence time estimations. The results demonstrate the conspecificity of D. v. emeraldi and D. midori, as well as the conspecificity of the entire complex under the name D. viridis due to the absence of significant morphological and molecular differences. We also identified previously undescribed species from the Kuril Islands, Diaphoreolis shinkaii sp.nov., which differs markedly from other Diaphoreolis species in its molecular, morphological, and bathymetric characteristics.

The Diversity of Lowland Representatives of the Highest‐Altitude Mammals: The Elusive Pikas of the Subgenus Alienauroa

Sat, 25 Apr 2026 01:34:50 -0700

ABSTRACT

The pikas of the subgenus Alienauroa were discovered merely 25 years ago, with the principal diversity of this group described only in 2017. This study integrates genomic, morphological, and distributional data from all specimens collected to date to advance the understanding of phylogeny, taxonomy, and distribution within these pika species. Our analyses delineate four distinct species: O. syrinx, O. sacraria, O. huanglongensis, and O. flatcalvariam. The entire group is restricted to a limited geographic area situated between the Huanghe and Yangtze rivers. All species exhibit strict ecological association with dark coniferous forests. Two sister species, O. syrinx and O. sacraria, display disjunct distributions and significant genetic divergence, indicative of relict range fragmentation. In contrast, the second sister pair, O. huanglongensis and O. flatcalvariam, exhibit restricted distributions and lower levels of genetic variation. The species generally demonstrate allopatric distribution, with the exception of O. syrinx and O. sacraria in the Qinling and Dabashan mountains, where they exhibit sympatry.

Systematics of Marmosa Subgenus Micoureus With Emphasis in ‘rapposa’ Group (Didelphidae, Marmosini): Geographic Variation and Revalidation of M. budini

Mon, 13 Apr 2026 03:15:39 -0700

ABSTRACT

Micoureus is the most species-rich subgenus within the genus Marmosa. Conflicting arrangements regarding the number of species comprising this subgenus have been proposed and the validity of M. budini has been debated. Here, we used an approach integrating genetic and morphological data were conducted to reanalyze the ‘rapposa’ group, investigate its biogeographic context, and test the status of M. budini as a distinct species of the M. rapposa complex. One mitochondrial and one nuclear marker were sequenced to recover species trees; divergence data and population aspects were inferred from mitochondrial data. Museum specimens were examined, including holotypes. The biogeographic data suggest the diversification in the ‘rapposa’ group to be associated with tectonism in the Andes and the Pebas System. Genetic analysis and external and craniodental morphology differences corroborate the species status of M. budini, with new record for Rondônia, Brazil, and M. rapposa would remain restricted to Peru. Marmosa rutteri exhibits intrapopulation variations driven by habitat fragmentation in the Pleistocene cycles and fluvial formations of the Amazon, and the separation in relation to M. budini coincides with climatic oscillations of the Late Quaternary and the Ucayali River.

Interplay Between River Formation and Historical Climatic Changes Drove Diversification of the Thamnomanes caesius and T. schistogynus (Passeriformes, Thamnophilidae) Species Complex Across Amazonian and Atlantic Forests

Thu, 09 Apr 2026 01:57:26 -0700

ABSTRACT

The Amazon and Atlantic forests harbour immense biodiversity shaped by complex evolutionary history with diverse processes leading to species build-up. We investigated the Cinereous Antshrike species complex (Thamnomanes caesius and T. schistogynus) to disentangle the relative contributions of riverine barriers and historical climatic fluctuations to diversification, using large specimen sampling across their entire distribution and a multilocus dataset. Our results revealed hidden genetic diversity, with 13 geographically structured phylogroups largely concordant with Amazonian interfluves and areas of endemism. Species delimitation analyses supported eight of these lineages as independently evolving units, unveiling cryptic diversity within T. caesius. Divergence time estimates indicate that diversification took place during the Pliocene to Late Pleistocene, with signatures of demographic expansion consistent with climate-driven range dynamics. Our findings underscore a strong association between phylogroups and major river systems, revealing their role as primary drivers of lineage diversification, later modulated by demographic shifts associated with climatic oscillations. Our findings highlight an interplay between geomorphological and climatic factors in shaping avian diversity across the Amazon basin, while also pointing to underestimated taxonomic richness within the Thamnomanes caesius/schistogynus species complex.

Issue Information

Mon, 06 Apr 2026 22:41:56 -0700

Zoologica Scripta, Volume 55, Issue 3, Page i-iv, May 2026.

A Comprehensive Morphological Description and Phylogenetic Analysis of First Instar Larvae: Clarifying the Intergeneric Relationships of Microfalcula, Salina and Akabosia (Collembola: Entomobryidae)

Jincheng Lu, Zhihong Zhan, Feng Zhang — Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

Considerable controversy has long surrounded Paronellidae. Previous morphological studies suggested a close connection between Microfalcula and Salina; concurrently, molecular phylogenetic analyses have indicated a closer relationship between Salina and Akabosia. However, a comprehensive analysis encompassing all three genera has been limited, leaving their precise interrelationships unclear. This study comprehensively examines and describes the first instar larval characteristics (antennae, dorsal cephalic chaetotaxy, labial chaetotaxy, leg, tergal chaetotaxy, ventral tube, tenaculum and furcula) of all three genera. We then reconstructed phylogenetic trees primarily based on dorsal chaetotaxy and other features. Our study suggested that these three genera belong to a single clade, forming the sister taxa between Salina and Akabosia. We identified five key morphological features supporting the monophyly of these three genera: absence of scales, enlarged tenent hairs, discrete eyes, unilobed antennal bulbs and reduced tergal S-chaetae from Th. II to Abd. III (10|000 in Microfalcula, 11|000 in Akabosia and 11|001 in Salina). Additionally, tergal chaetotaxy strongly supports a sister group relationship between Salina and Akabosia. This study partially supports and successfully validates the Entomobryidae taxonomic framework, affirming that primary chaetotaxy is a robust and comparable morphological characteristic for Collembola classification.

Drainage Basin Formation as a Key Driver of Diversification in Neotropical Aquatic Frogs

Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

The Neotropics are one of the most biodiverse regions in the world, yet the processes driving this diversity remain poorly understood. This study explored the spatio-temporal diversification of Pseudis paradoxa and Pseudis platensis, two closely related aquatic frog species associated with rivers and floodplains throughout South America. We addressed two questions: (1) How were the hypothetical ancestors of the P. paradoxa + P. platensis clade distributed? and, (2) What biogeographic processes influenced the diversification and current geographic distribution of the clade? Using two mitochondrial and three nuclear markers, we conducted lineage delimitation, divergence time estimation, and historical biogeography with BIOGEOBEARS. Results showed that both species consist of multiple lineages. The initial divergence was estimated at around 4.8 million years ago (2.8–7.2 Mya), at the Miocene–Pliocene transition. Ancestral range estimation recovered the origin of the P. paradoxa/P. platensis clade in a paleo-region spanning the Amazon and La Plata basins. Vicariance processes split this ancestral range, leading to allopatric populations in each basin. The establishment of the modern Amazon Basin, shaped by river capture events approximately 4.9–5.6 Mya, was likely the key factor promoting the diversification of the P. paradoxa/P. platensis clade.

Weak Nuclear Divergence Despite Pronounced Mitochondrial Divergence Within a Widespread Desert‐Inhabiting Palearctic Lark (Aves: Alaudidae)

Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

The Bar-tailed Lark Ammomanes cinctura is a polytypic bird species with a wide distribution. One of its three subspecies, A. c. arenicolor, has previously been found to show deep mitochondrial divergence between its geographically most distant populations, from Morocco and Saudi Arabia, respectively. We applied an integrative approach using genome-wide single nucleotide polymorphisms (SNPs), mitochondrial DNA (mtDNA), morphological and bioacoustic data to investigate the evolutionary divergence within A. cinctura. We confirmed the existence of two distinct mitochondrial clades: one including samples from Morocco and Cape Verde Islands and the other including samples from Saudi Arabia and Iran. We estimated that these lineages diverged 2.14 million years ago (Mya). In contrast, we recovered shallow divergence in the nuclear SNPs (estimated split time: 0.08 Mya) between the samples from Cape Verde–Morocco versus Saudi Arabia–Iran, and population structure analyses favored a single genetic cluster. Analyses of museum specimens confirmed earlier statements that the eastern subspecies, A. c. zarudnyi, has slightly longer wing and tail than the two others, and that the three subspecies are slightly divergent in plumage. Finally, our analyses of vocalisations suggested that some geographical differences might exist, but the commonest song type is found across the range. The reasons for the considerably deeper divergence in mitochondrial DNA relative to that of nuclear SNPs are unresolved and will require more comprehensive sampling to elucidate.

Evaluating Bayesian Morphological Clocks for Estimating a Dated Phylogeny in a Relict and Fossil‐Rich Family of Wasps (Hymenoptera, Chrysidoidea)

Anderson Lepeco, Gabriel A. R. Melo, Brunno B. Rosa — Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

In recent years, a wide array of tools originally developed for molecular dating analyses has been adapted for use within a morphological clock perspective. This is of paramount relevance for taxonomic groups that cannot be sampled in forms suitable for DNA extraction. The Scolebythidae, a small family of stinging wasps, represents an interesting group to study the application of the morphological clock due to their limited extant diversity contrasted with their abundant Cretaceous fossil record. Here, we investigate the impact of model specifications on the Bayesian inference of dated phylogenetic trees for the family. A total of 78 models were evaluated through Bayes Factors, with a thorough comparison of topology and node ages across the resulting trees. We find that the partitioning of characters had slight effects on ages retrieved, even though partitioning by homoplasy improved model fit and yielded narrower ranges for age estimates. The uniform tree prior consistently provided older age estimates compared to the fossilised birth-death prior. Models employing an Independent Gamma Rates (IGR) clock and lognormally distributed rate resulted in higher marginal likelihood values. While calibration priors had limited impact, the root age prior substantially affected both the estimates and overall model performance. We discuss the evolutionary history and biogeography of Scolebythidae, highlighting the relevance of dispersal events in shaping their modern disjunct distribution. Advances in the application of the morphological clock may be essential for bridging the extant diversity with the ever-growing fossil record.

Wing Patterns of Diversification: Phylogeny and Biogeography Reveal the Evolutionary History of the Raspy Cricket Genus Homogryllacris (Orthoptera: Gryllacrididae)

Yueting Duan, Yanhao Duan, Qidi Zhu, Zhijun Zhou, Fuming Shi — Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

The genus Homogryllacris Liu, 2007, with its diverse wing forms, represents a unique group within the family Gryllacrididae. Although significant progress has been made in understanding its species diversity in recent years, several problems remain unresolved. In this study, species delimitation was conducted using four molecular methods based on the mitochondrial COI gene fragment. Phylogenetic analysis, biogeographical and wing-form evolution studies were performed using three mitochondrial genes (COI, 16S rRNA and Cytb) and two nuclear genes (18S rRNA and 28S rRNA). Key findings include: (I) Species delimitation identified 19 valid species, including one new species, Homogryllacris eremna Duan, Duan & Shi sp. n., with Homogryllacris unicolor Lu, Zhang and Bian, 2022 syn. n. proposed as a synonym of Homogryllacris anelytra Shi, Guo and Bian, 2012; (II) The monophyly of this genus has been conclusively demonstrated, while our results reveal that wingforms and geographic distribution may not reliably reflect interspecific phylogenetic relationships; (III) The genus likely originated in the late Oligocene in the Yunnan-Guizhou Plateau and Southern Yunnan, with early lineage divergence potentially driven by activity of the Red River fault zone. Geographic isolation and Miocene climate changes jointly promoted lineage diversification, with the Yunnan-Guizhou Plateau and Southern Yunnan region serving as the center of differentiation and distribution; (IV) The ancestor of this genus was macropterous, with micropterous or brachypterous forms having evolved independently multiple times. Stable and favourable living conditions in the Miocene were likely the driving factors behind wing reduction in species of this genus.

Biogeographic Barriers and Historic Climate Shape the Genetic Structure and Demography of the Freshwater Crab (Brachyura, Potamidae) in Continental‐Island Systems

Ruxiao Wang, Meijun Liu, Ruyi Jin, Boyang Shi, Hongying Sun, Da Pan — Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

Island biogeography provides a crucial framework for interpreting global biodiversity patterns; however, the distinctive dynamics of continental islands remain underexplored relative to those of volcanic oceanic islands. This knowledge gap obscures our understanding of species dispersal and evolution, particularly on small continental islands whose connectivity has been modulated by Quaternary sea-level oscillations. Here, we integrate double-digest restriction-site-associated DNA (ddRAD) sequencing with mitochondrial COI and 16S rRNA data to investigate the phylogeography, population structure, demographic history and ecological niche of the narrowly distributed freshwater crab Nanhaipotamon nanriense inhabiting mainland and nearby islands in southeastern China. Our analyses revealed strong genetic differentiation, highlighting a deeply divergent island lineage isolated by a narrow marine channel and an inland lineage isolated by the Minjiang River. Demographic reconstructions indicated significant population expansions during lower sea level in the Pleistocene, followed by population contractions correlated strongly with post-glacial sea level rise in the Holocene. By synthesising genomic, demographic and ecological evidence, our study demonstrates how marine inundation, riverine barriers and glacio-eustatic cycles jointly shape the genetic and distributional patterns of continental island freshwater species and also provide critical insights for conservation strategies.

Phylogeographic Structure and Codivergence of Ceroplastes rubens (Hemiptera: Coccidae) and Its Fungal Symbiont in China

Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

Hemipteran insects typically rely on lineage-specific bacterial symbionts to meet their nutritional needs. However, soft scales (Hemiptera: Coccidae) are unique, with fungal rather than bacterial dominant symbionts. While bacterial symbioses in Hemiptera have been widely studied, fungal symbionts remain poorly understood. In this study, we investigated the red wax scale Ceroplastes rubens, a major pest of ornamental plants, by analysing 260 samples collected from 47 locations across 14 provinces in China between 2010 and 2023. We sequenced mitochondrial COI and nuclear 28S genes of the host and ITS and EF-1α genes of its fungal symbiont, Ophiocordyceps (Hypocreales, Ophiocordycipitaceae). Phylogenetic reconstruction revealed four geographically distinct lineages of C. rubens in southern China, shaped by biogeographic barriers, host plant variation, and historical climate patterns. Each lineage harboured a specific Ophiocordyceps clade, exhibiting strong phylogenetic congruence. Cophylogenetic analyses revealed a significant association between the host and its fungal symbiont, supporting the parallel evolution hypothesis. Divergence time estimates suggested that the Ophiocordyceps symbiont associated with C. rubens originated after its host and subsequently underwent codiversification. This study provides the most comprehensive phylogenetic framework to date for scale insects and their fungal symbionts, offering novel insights into the evolution of obligate symbioses in Hemiptera.

Molecular Phylogeny, Species Delimitation, and Biogeography of the Varunid Crab Genus Metaplax (Crustacea, Varunidae)

Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

The Indo-West Pacific genus Metaplax comprises 11 recognised species inhabiting intertidal mudflats, some adjacent to mangroves. To resolve long-standing uncertainties, we analysed mitochondrial (COI, 16S) and nuclear (28S) markers. Phylogenetic analyses recovered Metaplax as monophyletic and resolved four well-supported clades—the M. distincta, M. elegans, M. crenulata and M. indica clades—corroborated by morphology. COI barcoding delimited all 11 species, with intraspecific distances ≤ 2.01% and interspecific distances ≥ 5.76%, establishing a clear barcode gap. Molecular-clock estimates date the split of Metaplax from other varunids to ca. 31.6 Ma, with subsequent diversification into four clades between 29.8 and 26.3 Ma. Ancestral-range reconstructions support an Indian Ocean origin followed by stepwise dispersal into the western Pacific. These findings clarify interspecific relationships, confirm the utility of COI for Metaplax species delimitation, and suggest an Indian Ocean origin with later west-to-east expansion.

The Phylogenetic Position of the Extinct Hawaiian Honeyeaters: Overcoming the Limitations of Historical DNA

Min Zhao, Rebecca T. Kimball, Edward L. Braun — Mon, 06 Apr 2026 22:41:56 -0700

ABSTRACT

Mohoidae, the Hawaiian honeyeaters, are a group of extinct birds that once inhabited the Hawaiian Islands. Their genetic data are only available from historical museum specimens, so it is based on highly fragmented and damaged DNA. Sequences assembled from historical specimens can have large amounts of missing data and they often result in exceptionally long terminal branches in phylogenies. These long branches can distort estimates of phylogeny, an artifact known as long branch attraction. However, the best way to analyse this data is unclear because these long branches are typically artifactual, reflecting DNA quality. We investigated the position of Mohoidae within the superfamily Bombycilloidea using published alignments of ultraconserved elements (UCEs) and re-assembled UCEs from raw sequencing reads. The uncertainty involves two monotypic families (Hypocoliidae and Hylocitreidae). Re-aligning UCEs using a smaller taxon set closely related to Mohoidae, along with edge trimming and re-assembly, eliminated the long branches of Mohoidae and Hypocoliidae (also represented by a historical sample). The sister relationship of these two families in previous studies appears to be artifactual; our new analyses yielded congruent topologies that placed Mohoidae as sister to a clade comprising Hypocoliidae and Hylocitreidae. We also found that different assemblers (SPAdes vs. Trinity) yielded sequences with conflicts towards the ends of the UCEs, especially for the historical samples, although this did not alter the topology. Finally, combining the UCEs with traditional Sanger sequencing data allowed us to produce a strongly supported complete phylogeny of Bombycilloidea that included all extant species as well as the extinct Mohoidae.

Progress and Challenges in Phylogenomics and Genomics of Lophotrochozoa/Spiralia

Torsten H. Struck — Sat, 04 Apr 2026 00:59:52 -0700

ABSTRACT

Lophotrochozoa is one of the three major bilaterian groups comprising more than half of the bilaterian phyla. Lophotrochozoa includes among others Mollusca, Annelida, Platyhelminthes and Rotifera. Despite representing such a large proportion of animal diversity, they are historically understudied and genomic resources have been scarce. However, the last years have seen a strong increase of genomic resources due to the initiatives associated with the Earth Biogenome Project. Hence, herein I will review the progress made with respect to the available genomic resources for Lophotrochozoa and its phylogeny based on genome-scale data. With several hundreds of chromosome-level genomes available for Lophotrochozoa, tremendous progress has been achieved. However, tissue availability in relation to the genome size remains a major challenge and genomic information for small-sized lophotrochozoan taxa like Gnathostomulida and Entoprocta are still missing on a large scale. Hence, a major challenge remains to obtain enough high-quality DNA despite recent progresses in whole-genome amplification methods. Summarizing recent phylogenomic studies showed that monophyletic Chaetognathifera is sister to the remaining Lophotrochozoa, known as Platytrochozoa. Within Platytrochozoa, Rouphozoa, Entoprocta + Cycliophora, Lophophorata and Bryozoa + Phoronida can be recognized as monophyletic, but other relationships are contentious. Moreover, to date, no phylogenomic study has sampled all lophotrochozoan phyla. Reviewing macrosyntenic studies and patterns across Lophotrochozoa reveals that its potential as a phylogenetic marker might be much more limited than expected. The analyses show very high degrees of convergent evolution, in part due to massive fusion events. Hence, convergent evolution of fusion-with-mixing events might be more rampant than assumed at present.

Profundum solomoni (Amphipoda: Uristidae) Exhibits a Disjunct Geographic Distribution at Hadal Depths Across the San Cristobal Trench, Santa Cruz Trench and Nova Canton Trough

Brett C. Gonzalez, Jennifer A. Wainwright, Alan J. Jamieson — Wed, 25 Mar 2026 03:16:05 -0700

ABSTRACT

Hadal environments (> 6000 m ocean depths) are often viewed as isolated locations with high species endemism due to limited dispersal. However, molecular studies continue to reveal greater complexity that questions historical perceptions. Recent population genetic studies focused on scavenging amphipods have identified broadly distributed lineages spanning multiple hadal features, challenging hadal endemism. Here, we investigate the morphological and genetic diversity of the recently erected hadal amphipod Profundum solomoni (Uristidae) from three features in the South Pacific. Integrating three widely utilised delimitation approaches (GMYC, PTP, ABGD), our multilocus analyses overarchingly converge on a single evolutionary lineage throughout the neighbouring San Cristobal Trench, Santa Cruz Trench and Nova Canton Trough ~3000 km to the east. Demographic statistics and COI haplotype networks further indicate a recent population expansion with little evidence of ongoing gene flow. Together, these results demonstrate an unusual distribution of P. solomoni as to date they have not been found in the New Britain, New Hebrides, Kermadec and Tonga trenches which are geographically closer to where they were found here. This study adds to the growing number of lysianassids reported from multiple hadal features across ocean basins.

Phylogeny and Species Delimitation in the Land Snail Genus Chilostoma (Gastropoda: Helicidae) and East–West Alpine Disjunctions

Elisa Becher, Bernhard Hausdorf — Fri, 20 Mar 2026 02:05:58 -0700

ABSTRACT

Chilostoma includes large, mostly rock-dwelling snail species, widespread in the European Alps and the Apennines in Italy. We analysed the phylogenetic relationships and the species delimitation of the Chilostoma (Chilostoma) species based on genomic ddRAD loci. The Chilostoma (Chilostoma) taxa form three sister pairs. Chilostoma achates and C. zonatum are a vicariating East–West Alpine sister species pair, the sister group of all other Chilostoma (Chilostoma) species. The high Alpine taxa C. hermesianum and C. liguricum, which were previously classified as subspecies of C. (Cingulifera) cingulatum, form another East–West Alpine pair, belonging to C. frigidum. The sister group of C. frigidum comprises C. foetens and C. tigrinum. Chilostoma foetens includes the genetically and morphologically variable populations from the Bergamasque Prealps classified so far as C. adelozona, the populations from the Rhaetian Alps (rhaeticum), and the populations from the Aosta Valley and the Lower Valais (foetens). The latter population groups are nested in the populations from the Bergamasque Prealps. The population of C. tigrinum from the Cottian Alps is nested in the populations from the Bergamasque Prealps. There are also several East–West Alpine disjunctions in other land snail taxa. These disjunctions are partly caused by a gap of limestone between the Bergamasque Prealps and the Maritime and Ligurian Alps. The crystalline rocks in this region are not suitable for all land snail species. The East–West Alpine disjunctions are remnants of larger distribution ranges, or of long-distance dispersal events from the east to the west.

High Evolutionary and Taxonomic Diversity of Gerbils (Gerbillus) in the Horn of Africa

Mon, 16 Mar 2026 00:00:00 -0700

ABSTRACT

The genus Gerbillus represents a striking example of successful Pleistocene radiation among rodents, resulting in nearly 50 currently recognised species distributed across Asia (from the Middle East to northwestern India) and Africa (the Saharo-Sahelian region and eastern Africa). Over the past two decades, multiple molecular phylogenetic studies have helped elucidate the complex subgeneric structure of this speciose group. Here, by incorporating into a genetic analysis of mitochondrial and nuclear markers and using samples collected in Somaliland, Ethiopia, Kenya and Tanzania, together with available GenBank sequences of other Gerbillus species we provide, for the first time, genetic data for Microdillus peeli (a taxon whose phylogenetic position has remained unresolved for over a hundred years) and unequivocally demonstrate that it represents an internal lineage within Gerbillus. In addition, we characterise a novel lineage within the genus and attempt to decipher its phylogeographic structure. However, having failed to discriminate between genetically defined lineages using geometric morphometrics and owing to the lack of genetic data for several critically important specimens, we do not undertake a taxonomic revision or describe new taxa within the scope of the present study.

Evolution and Biogeography of the Genus Heteropoda (Heteropodinae: Sparassidae) Across Southeast Asia

Thu, 05 Mar 2026 21:22:23 -0800

ABSTRACT

Heteropoda huntsman spiders are large, fast-moving predators widely distributed across tropical and subtropical regions, where they function as important nocturnal hunters. Despite their ecological prominence, the evolutionary and biogeographic history of the genus remains poorly resolved. Here, we analysed a six-locus dataset (two mitochondrial and four nuclear genes) to estimate divergence times and reconstruct ancestral ranges within Heteropoda using Bayesian phylogenetic and statistical biogeographic approaches, and we assessed broad climatic suitability using genus-level ecological niche modelling. Time-calibrated analyses support the monophyly of Heteropoda and indicate that crown diversification began during the early Oligocene (~30 Ma; 95% HPD: 18–41 Ma). A primary split between Australasian and Asian lineages is inferred near the Oligocene–Miocene transition (~23 Ma; 95% HPD: 14–33 Ma), followed by radiation within Southeast and East Asia. Ancestral-area reconstructions consistently recover Australasia as a key ancestral component and suggest repeated dispersal and isolation across the Sunda–Wallacea interface under conditions of long-term tectonic instability. Ecological niche modelling identifies temperature, precipitation, and elevation as major correlates of climatic suitability, consistent with the predominance of Heteropoda in warm and humid environments. Together, these results provide an integrated temporal, spatial, and ecological framework for understanding diversification and present-day distribution of Heteropoda across Southeast Asia and adjacent regions.

Evolution of Crematogaster sordidula (Hymenoptera, Formicidae) Ants in the Mediterranean Region During Plio‐Pleistocene Climatic Changes

Tue, 03 Mar 2026 04:31:20 -0800

ABSTRACT

Understanding insect responses to global climate change involves identifying strategies used during past climate oscillations. Phylogeography offers a powerful framework to unravel how historical climatic and geological events have shaped the spatial genetic patterns of species, providing critical insights into evolutionary processes, whereas population genomic approaches enable finer-scale resolution of demographic history and genetic connectivity. We focus on an abundant ant species, Crematogaster sordidula, endemic to the Mediterranean region, a biodiversity hotspot experiencing faster warming than the global average. Using a phylogenomic dataset of ultraconserved elements (UCEs) from 123 individuals, we reconstructed population-level relationships with maximum-likelihood and coalescent methods and estimated a time-calibrated phylogeny to investigate the timing of major divergence events. We inferred population structure by generating mitochondrial haplotype networks and analysing admixture and regional genetic diversity and differentiation on the basis of SNPs obtained from UCE data. We recovered four major lineages that diverged during the Pliocene: a Western Mediterranean clade, an Eastern Aegean region clade, an Anatolia-Türkiye clade, and a Central-Eastern Mediterranean clade, with the latter three together forming a larger Eastern Mediterranean clade. This population structure confirms the east–west distribution pattern found for many taxa in the Mediterranean. Genetic diversity was highest in southern regions, supporting the hypothesis that these areas acted as refugia during Pleistocene climatic oscillations. Within the Eastern Mediterranean clade, population structure and gene flow indicate complex demographic histories possibly shaped by the region's dynamic palaeogeography and paleoclimatic history. Together, these results provide a foundation for understanding the species' potential responses to ongoing environmental changes.

Multilocus Phylogeny Reveals New Species From the Ancient Lake Fuxian and Synonymy of Cipangopaludina With Margarya (Gastropoda: Viviparidae)

Tue, 03 Mar 2026 04:21:03 -0800

ABSTRACT

The ancient lakes of Yunnan Province, China, harbour a highly diverse and endemic assemblage of viviparid freshwater snails. Based on analyses of partial mitochondrial genes (COI, 16S), nuclear markers (18S, 28S rDNA and H3) and mitogenomes, here we reconstruct the most complete time-calibrated phylogeny and mitogenomic phylogeny of river snail genus Margarya and Cipangopaludina. Based on the comprehensive molecular and morphological evidence, we propose the following taxonomic revisions: Cipangopaludina Hannibal 1912 is treated as a junior synonym of Margarya (syn. nov.), and Margarya francheti (Mabille, 1886) is regarded as a junior synonym of Margarya melanioides Nevill, 1877 (syn. nov.). Furthermore, Cipangopaludina haasi Prashad, 1928 (syn. nov.), Dalipaludina pyramidella (Du, Yang and Chen, 2011) (syn. nov.) and Cipangopaludina ventricosa (Heude, 1890) (syn. nov.) are assigned as junior synonyms of Margarya compactus (Nevill, 1869) (comb. nov.), while Cipangopaludina hehuensis Lu, Fang and Du, 2016 (syn. nov.) is considered a junior synonym of Margarya chinensis (Grey, 1833) (comb. nov.). In addition, this study describes two new species within the genus Margarya from ancient lakes in Yunnan: Margarya caiyun Zheng, He, Xiang, Zhang and Wu sp. nov. and Margarya feihu Zheng, He, Xiang, Zhang and Wu sp. nov. Phylogenetic analyses reveal an Oligocene origin for Margarya and resolve three highly supported clades, whose diversification is closely linked to the dynamic geological history of the Yunnan Plateau. This study highlights the urgent need for conservation of these endemic snails and their imperilled lacustrine habitats.

The Role of Gene Flow in the Diversification of the Monkey Treefrog Complex Across the South American Dry Diagonal

Wed, 04 Feb 2026 02:34:25 -0800

ABSTRACT

Understanding Neotropical megadiversity remains challenging due to fundamental taxonomic issues, including identifying and describing cryptic species and their distribution, and the limited knowledge of key factors driving biological diversification. Such challenges are especially prominent in diverse clades with high levels of cryptic species, such as many Neotropical frogs. Herein, we conduct a mitochondrial phylogenetic study on monkey treefrogs in the genus Pithecopus and a multilocus analysis of the P. hypochondrialis species group throughout its distribution in the South American dry diagonal (DD). Our goals were to infer the main lineages and identify historical factors that led to their divergence. Among nine currently recognised species, we found 14 well-structured mitochondrial lineages in two main clades, which diversified during the Paleogene/Neogene transition. The lowland clade is widely distributed in the DD, and our multilocus analysis suggests it comprises seven geographically structured lineages: P. azureus, two lineages of P. hypochondrialis, two species and one lineage for the P. nordestinus complex, and Pithecopus sp. Considering the geomorphological history of the region, diversification may have been promoted by allopatric speciation during Miocene paleogeographic events, especially the Brazilian Plateau compartmentalization and fluctuations in the São Francisco River water volume. Furthermore, gene flow between some lineages may be explained by niche conservatism and demographic expansions during the late Pleistocene, a period marked by climatic fluctuations and biome shifts. Our results reinforce the importance of both Neogene tectonic activity and Quaternary climatic fluctuations in shaping the Neotropical biota.