| 1. |
- Aurelle, Didier, et al.
(författare)
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On the specific status of eastern Mediterranean Dendrophyllia corals (Cnidaria, Anthozoa): Genetic characterization and speciation scenarios
- 2024
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Ingår i: Zoologica Scripta. - 0300-3256 .- 1463-6409. ; 53:2, s. 235-247
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Tidskriftsartikel (refereegranskat)abstract
- The deep-sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to D. ramea but had some morphological differences with other known populations of this species. Here, we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two Caryophyllia species. Both morphological and genetic data confirm that corals found off Cyprus belong to the D. ramea species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species.
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| 2. |
- Bachmann, L., et al.
(författare)
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The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022
- 2023
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 52:3, s. 187-214
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Tidskriftsartikel (refereegranskat)abstract
- On 25 August 2022, the Zoologica Scripta - An International Journal of Systematic Zoology and the Norwegian Academy of Sciences and Letters arranged a symposium entitled 'The role of systematics for understanding ecosystem functions' in the Academy's premises in Oslo, Norway. The symposium aimed at offering a forum for exploring and discussing trends and future developments in the field of systematics. Eleven international experts contributed expertise on various issues related to global challenges, such as biodiversity assessments, databases, cutting-edge analysis tools, and the consequences of the taxonomic impediment. Here, we compiled a multi-author proceedings paper of the symposium contributions that are arranged in chapters and presents the content and the key conclusions of the majority of the presentations.
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| 3. |
- Bassitta, Marta, et al.
(författare)
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Multilocus and morphological analysis of south-eastern Iberian Wall lizards (Squamata, Podarcis)
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 49:6, s. 668-683
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south-east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear markers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in species delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera lineage from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.
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| 4. |
- Erséus, Christer, 1951, et al.
(författare)
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Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 49:5, s. 614-640
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Tidskriftsartikel (refereegranskat)abstract
- Clitellata is a major clade of Annelida comprising nearly all freshwater and terrestrial annelids as well as several marine species. We investigated clitellate phylogenetic relationships using transcriptomes sampled from 74 taxa (64 clitellates and 10 polychaetes), including multiple representatives of nearly all major clitellate higher taxa (Branchiobdellida, Capilloventridae, Crassiclitellata, Enchytraeidae, Haplotaxidae, Hirudinida, Lumbriculida, Moniligastridae, Naididae, Parvidrilidae, Phreodrilidae, Propappidae and Randiellidae). We used a number of filtered data matrices and phylogenetic analyses to examine the effects of data partitioning, missing data and compositional and branch-length heterogeneity and used the resulting phylogenies for divergence time estimation and ancestral habitat reconstructions. All analyses and filtering methods produced a consistent, strongly supported topology in which (a) Enchytraeidae, Hirudinida, Hirudinea (here, Branchiobdellida plus Hirudinida), Lumbriculida, Lumbriculata (Lumbriculida plus Hirudinea), Phreodrilidae and Naididae are monophyletic, (b) a Parvidrilidae + Randiellidae clade is sister to the rest of Clitellata, (c) Phreodrilidae is sister to Naididae, (d) Haplotaxidae is non-monophyletic, with some haplotaxids grouping with Crassiclitellata + Moniligastridae, (e) the Phreodrilidae + Naididae clade is sister to all other clitellates except Parvidrilidae + Randiellidae and Capilloventridae, and (f) Lumbriculata is sister to the Crassiclitellata + Moniligastridae + Haplotaxidae (in part) clade. Ancestral habitat reconstructions and divergence time analysis suggested that the most recent common ancestor of Clitellata lived in freshwater during the Devonian (419-359 million years ago) and that all major extant clitellate lineages arose over the next similar to 150 million years, with multiple lineages subsequently returning to marine habitats or invading land. This study provides a phylogenetic framework for further investigation of the geological, environmental and biotic forces and genomic changes that may have impacted clitellate evolution and enabled several major habitat transitions within this group.
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| 5. |
- Ghanavi, Hamid Reza, et al.
(författare)
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The (non) accuracy of mitochondrial genomes for family-level phylogenetics in Erebidae (Lepidoptera)
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 51:6, s. 695-707
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Tidskriftsartikel (refereegranskat)abstract
- The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenetic studies. Now with the appearance of genomic scale data, increasing number of mitochondrial genomes are available, leading to an increasing number of mitophylogenomic studies. Here, we assemble 47 mitochondrial genomes using whole genome Illumina short reads from representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily-level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships.
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| 6. |
- Ghorbani, F., et al.
(författare)
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Densely sampled phylogenetic analyses of the Lesser Short-toed Lark (Alaudala rufescens) - Sand Lark (A. raytal) species complex (Aves, Passeriformes) reveal cryptic diversity
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409.
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomy of the Lesser/Asian Short-toed Lark Alaudala rufescens-cheleensis complex has been debated for decades, mainly because of minor morphological differentiation among the taxa within the complex, and different interpretations of the geographical pattern of morphological characters among different authors. In addition, there have been few studies based on non-morphological traits. It has recently been suggested based on a molecular study of the lark family Alaudidae that the Sand Lark A. raytal is nested within this complex. We here analysed mitochondrial cytochrome b (cyt b) from 130 individuals across the range of this complex (hereafter called Alaudala rufescens-raytal complex), representing all except two of the 18 currently recognized subspecies. We also analysed 11 nuclear markers from a subsample of these individuals, representing all of the clades found in the cyt b tree. Five primary clades were recovered, which confirmed that A. raytal is nested within this complex. Divergence time estimates among these five clades ranged from 1.76 to 3.16 million years (my; 95% highest posterior density [HPD] 1.0-4.51 my) or 1.99-2.53 my (95% HPD 0.96-4.3 my) in different analyses. Only four of the currently recognized subspecies were recovered as monophyletic in the cyt b tree. Our results call for a taxonomic revision, and we tentatively suggest that at least four species should be recognized, although we stress the need for an approach integrating molecular, morphological and other data that are not yet available.
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| 7. |
- Hamdan, B., et al.
(författare)
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A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes, Viperidae)
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 49:2, s. 145-158
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Tidskriftsartikel (refereegranskat)abstract
- Based on the literature, we had predicted that the diversification within the Neotropical snake genus Bothrops occurred along a latitudinal gradient from north to south, with diversification into unoccupied niches through ecological opportunity, not correlated with geoclimatic events. Using a dated phylogeny and estimating likelihoods of ancestral states at cladogenesis events, we reconstructed ancestral areas and assessed major events of the diversification of Bothrops clades, and we also discuss systematic implications for this group. Based on the phylogeny we produced, B. lojanus was not considered as part of the genus Bothrops since the results recovered this species nested within the Bothrocophias clade. We infer that the diversification of the Miocene Bothrops pictus and Bothrops alternatus clades may be related to the uplift of the western slopes of the Andes and the Argentinian Patagonian Andes, respectively. The Pliocene Bothrops taeniatus and Bothrops osbornei clades may be related to the uplift of the eastern and northern Andes, respectively. The Plio-Pleistocene Bothrops neuwiedi clade may be related to the habitat transitions from a warmer and forested environment to a cooler and open landscape; the Bothrops jararaca (i.e. island endemic species) and Bothrops lanceolatus clades to over-water dispersal with island speciation; and Bothrops atrox clade to the appearance of the Panamanian land bridge. We found that a multitemporal and multidirectional history of diversification may be correlated with geoclimatic and dispersalist events. We argue that the vacant niche hypothesis by itself does not explain Bothrops diversification.
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| 8. |
- Kalthoff, Daniela C., et al.
(författare)
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Incisor enamel microstructure places New and Old World Eomyidae outside Geomorpha (Rodentia, Mammalia)
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 51:4, s. 381-400
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Tidskriftsartikel (refereegranskat)abstract
- The lower incisor enamel microstructure of the fossil rodent family Eomyidae was believed to be three-layered and highly derived but rather uniform throughout the clade. Here, we describe a new four-layered schmelzmuster in Eomyidae consisting of a three-fold portio interna with longitudinal oriented, uniserial Hunter-Schreger bands and a one-fold portio externa, accounting for a unique enamel microstructure character combination in Rodentia. This new schmelzmuster type has developed early in eomyid evolution and is detectable already in the late Eocene (Chadronian) of North America. In European eomyids, it first occurs in the early Miocene (MN 3), implying that this four-layered schmelzmuster was not present in all members of the family but restricted to species included in Eomyini and some genera currently considered Eomyidae incertae sedis within Eomyidae. Additionally, our analysis recognizes three taxa with schmelzmuster divergent from all other eomyids. Incisor enamel microstructure does not advocate a close phylogenetic relationship of Eomyidae to either fossil or extant Heteromyidae and Geomyidae, nor to fossil Heliscomyidae and Florentiamyidae. Our results rather support the view that Eomyidae are placed outside Geomorpha.
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| 9. |
- Mohammadi, Z., et al.
(författare)
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Multilocus phylogeny reveals habitat driven cryptic diversity in Ochotona rufescens (Ochotonidae)
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 51:6, s. 617-28
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Tidskriftsartikel (refereegranskat)abstract
- Taxonomy of Afghan pikas Ochotona rufescens distributed in Western and Central Asia has long been debated, and the presence of cryptic diversity within the species has been suggested. In this study, we used one mitochondrial (cyt b) and six nuclear (nuDNA) markers to investigate genetic diversity within Afghan pikas O. rufescens populations based on 54 new samples from Western and Central Asia. In total, we included 200 new sequences of mitochondrial cyt b and six nuclear markers from 60 samples. Our results reveal a genetic split within Afghan pikas both in mitochondrial and nuclear markers, estimated to date back to at least 0.58 Mya, suggesting that two cryptic and isolated lineages exist among Afghan pikas in Western and Central Asia. Geographic patterns corresponding to known subspecies were largely corroborated. We hypothesize that during interglacials pikas are forced to track their habitat and move to higher elevations to avoid the desertification of the lowlands, effectively trapping them in refugia at the highest elevations. During glacials, cool climate may have created lowland habitats that pikas could tolerate, potentially allowing them to disperse between mountains. Pikas thus appear to be forced into refugia during the warmer climates of interglacials, rather than enduring ice ages in refugia, like most other organisms discussed in the context of Pleistocene refugia.
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| 10. |
- Moraes, Simeão de Souza, et al.
(författare)
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A double-edged sword : Unrecognized cryptic diversity and taxonomic impediment in Eois (Lepidoptera, Geometridae)
- 2021
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 50:5, s. 633-646
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Tidskriftsartikel (refereegranskat)abstract
- The genus Eois Hübner (Geometridae: Larentiinae) comprises 254 valid species. Being a hyperdiverse genus, Eois potentially includes many undescribed cryptic species and embodies a problematic taxonomic scenario. The actual diversity of Eois is greatly underestimated and the Neotropical fauna needs to be well known since it figures as one of the most threatened terrestrial ecosystem. In the present study, we compare three species delimitation methods to highlight the hidden diversity within a subset of Eois species: Automatic Barcode Gap Discovery, Bayesian Poisson Tree Processes and Multi-Rate Poisson Tree Processes. Our results point to an increase up to 176% in the currently valid species number. The hypothesis of cryptic diversity is corroborated by morphological characters within some species complexes. For complexes comprising species of Brazilian fauna, we provide a preliminary taxonomic assessment. Additionally, we found no congruence among the three delimitation methods for some species complexes, which indicates the importance of species and locality sampling as well as the previous alpha taxonomic knowledge in avoiding result bias. In this sense, we tried to standardize the identification provided for the Genbank sequences used in most relevant publications for Eois, in order to minimize biases and maximize the replicability of analyses in future studies. Moreover, we stress the importance of an integrative taxonomic approach for cryptic species discovery approach by employing both morphological attributes and life history to corroborate molecular analysis.
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