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Journal articles on the topic 'Divergent evolutionary lineage'

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Published: 5 June 2025

Last updated: 16 July 2025

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Lindsey, Laramie L., and Loren K. Ammerman. "Patterns of genetic diversification in a widely distributed species of bat, Molossus molossus." Occasional Papers Museum Texas Tech University, no. 339 (June 12, 2016): 1–16. https://doi.org/10.5281/zenodo.13448479.

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(Uploaded by Plazi for the Bat Literature Project) The taxonomy and evolutionary relationships of the Velvety Free-tailed Bat, Molossus molossus, from Central and South America long have been debated. Within this species, and in fact the entire genus Molossus, specimens have been difficult to identify and have presented several taxonomic challenges. The objective of this project was to characterize the genetic relationship among individuals representing subspecies of the widely distributed species, M. molossus. We tested the hypothesis that genetic patterns of diversification would reflect subspecies lineages. The mitochondrial gene cytochrome b (cytb) was amplified and sequenced for specimens throughout its geographic range. A Bayesian analysis of 678 base pairs of the cytb gene was conducted for 65 specimens with M. alvarezi as an outgroup. Our results showed that the subspecies M. m. daulensis, recognized based on morphology and geographic location, formed a statistically supported mitochondrial lineage in the phylogenetic analysis. However, not all currently recognized subspecies of M. molossus were recovered by this analysis. One lineage, M. m. tropidorhynchus from Cuba, formed a divergent monophyletic lineage. Overall, the average divergence across all specimens was 4.7%; however the M. m. tropidorhynchus lineage was 7.9% divergent from the other M. molossus specimens. This level of divergence and the recovery of a monophyletic lineage containing all Cuban specimens was consistent with recognition of the taxon as a distinct species.

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Lindsey, Laramie L., and Loren K. Ammerman. "Patterns of genetic diversification in a widely distributed species of bat, Molossus molossus." Occasional Papers Museum Texas Tech University, no. 339 (June 7, 2016): 1–16. https://doi.org/10.5281/zenodo.13448479.

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Lindsey, Laramie L., and Loren K. Ammerman. "Patterns of genetic diversification in a widely distributed species of bat, Molossus molossus." Occasional Papers Museum Texas Tech University, no. 339 (July 3, 2016): 1–16. https://doi.org/10.5281/zenodo.13448479.

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Lindsey, Laramie L., and Loren K. Ammerman. "Patterns of genetic diversification in a widely distributed species of bat, Molossus molossus." Occasional Papers Museum Texas Tech University, no. 339 (July 10, 2016): 1–16. https://doi.org/10.5281/zenodo.13448479.

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Vijayakumar, Seenapuram Palaniswamy, Robert Alexander Pyron, K. P. Dinesh, et al. "A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India." PeerJ 7 (March 12, 2019): e6457. http://dx.doi.org/10.7717/peerj.6457.

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The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinaesubfam. nov.(endemic to the WG, Peninsular India), and describe a new genusAstrobatrachusgen. nov.and species,Astrobatrachus kurichiyanasp. nov.The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.

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Liang, Junmin, Lorenzo Pecoraro, Lei Cai, et al. "Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha." Journal of Fungi 7, no. 12 (2021): 1088. http://dx.doi.org/10.3390/jof7121088.

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Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56–33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.

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Oliver, Paul, J. Scott Keogh, and Craig Moritz. "New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology." Australian Journal of Zoology 62, no. 6 (2014): 417. http://dx.doi.org/10.1071/zo14091.

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Species are a fundamental unit for all fields of biology but conceptual and practical limitations have hampered the process of identifying and describing species in many organismal groups. One outcome of these challenges is the accumulation of genetically divergent lineages and morphologically distinctive populations that are ‘known’, but remain of uncertain taxonomic status and evolutionary significance. These lineages are also currently not effectively incorporated into evolutionary studies or conservation planning and management. Here we suggest three ways to address this issue. First, there is a need to develop improved frameworks to systematically capture taxonomically unrecognised lineage diversity. Second, increased utilisation of metadata frameworks will allow better recording and dissemination of biodiversity information. Finally, emerging genomic and analytical techniques will provide powerful new tools to improve our identification and understanding of evolutionary lineages.

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Cheng, Lei, Cuiyun Lu, Le Wang, Chao Li, and Xiaoli Yu. "Coexistence of Three Divergent mtDNA Lineages in Northeast Asia Provides New Insights into Phylogeography of Goldfish (Carssius auratus)." Animals 10, no. 10 (2020): 1785. http://dx.doi.org/10.3390/ani10101785.

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Goldfish (Carassius aurautus), which is a middle size cyprinid, widely distribute throughout Eurasia. Phylogeographic studies using mtDNA markers have revealed several divergent lineages within goldfish. In this study, mtDNA variations were determined to elucidate the phylogeographical pattern and genetic structure of goldfish in Northeast Asia. A total of 1054 individuals from Amur river basin were analyzed, which including five newly collected populations and four previously reported populations. Three distinct mtDNA lineages were identified in those samples, two of which corresponded to two known lineages C2 and C6, respectively. The third lineage referred to as C7, following six known lineages of goldfish in mainland Eurasia. AMOVA results suggested that most of the genetic variations were among lineages, rather than among populations or twice samplings. We noted that the control region (CR) and cytochrome b (cytb) sequences of lineage C7 have been reported in previous studies, respectively. However, the evolutionary position and distribution pattern of this lineage was not discussed in the context of the species. Our results showed that “odd” CR and “hidden” cytb sequences from Central Asia represent the same mtDNA lineage of goldfish. The known samples of C7 lineage were collected from Central Asia (Eastern Kazakhstan and Western Mongolia) to East Asia (Northeast China and Far East Russia), which suggested that it had a wider distribution, rather than limit in Central Asia.

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Kukushkin, Oleg, Oleg Ermakov, Iulian Gherghel, et al. "The mitochondrial phylogeography of the Crimean endemic lizard Darevskia lindholmi (Sauria, Lacertidae): Hidden diversity in an isolated mountain system." Vertebrate Zoology 71 (October 6, 2021): 559–76. http://dx.doi.org/10.3897/vz.71.e62729.

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Abstract The Lindholm rock lizard, Darevskia lindholmi, is the only member of the genus Darevskia whose range is restricted solely to Europe, representing a local endemism found only in the Crimean Mountains. In our study, we investigated the cytochrome b gene (mtDNA) of 101 D. lindholmi sequences from 65 Crimean localities, representing its entire range. We found that D. lindholmi is highly genetically structured, and its range is divided into populations belonging to three mitochondrial lineages. The Lindholm rock lizard populations inhabiting the middle part of the Crimean Mountains (further referred to as the Central lineage) are sharply differentiated from the other two lineages (the Common and the Southwestern lineages), which are present in most of the species range. The genetic distance between the Central lineage and the other two taken together is 4.6%, according to our results, suggesting that the divergence occurred during the Early Pleistocene. The narrowly distributed Southwestern lineage and the widespread Common lineage, on the other hand, are differentiated by 1%. Field observations on the representatives of the main evolutionary groups show that their ecology is also different: the Central lineage is a mesophilic and cold-resistant form, while the other two closely related lineages are more xerophilic and thermophilic. Results of the potential ranges modeling and ecological niche analysis confirm that the genetic lineages occupy different niches of the Crimea. Furthermore, the area of inhabitation of the Central lineage splits the western and eastern parts of the Common lineage range, while the Southwestern lineage is restricted along the coast of the southwestern coast of the peninsula. The long-term co-existence of deeply divergent sister mitochondrial lineages in a relatively small (circa 7,000 km2) isolated mountain system serves as a mesocosm for understanding the speciation process. Our data suggest that the Central lineage warrants further taxonomic investigation.

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Abstract The Lindholm rock lizard, Darevskia lindholmi, is the only member of the genus Darevskia whose range is restricted solely to Europe, representing a local endemism found only in the Crimean Mountains. In our study, we investigated the cytochrome b gene (mtDNA) of 101 D. lindholmi sequences from 65 Crimean localities, representing its entire range. We found that D. lindholmi is highly genetically structured, and its range is divided into populations belonging to three mitochondrial lineages. The Lindholm rock lizard populations inhabiting the middle part of the Crimean Mountains (further referred to as the Central lineage) are sharply differentiated from the other two lineages (the Common and the Southwestern lineages), which are present in most of the species range. The genetic distance between the Central lineage and the other two taken together is 4.6%, according to our results, suggesting that the divergence occurred during the Early Pleistocene. The narrowly distributed Southwestern lineage and the widespread Common lineage, on the other hand, are differentiated by 1%. Field observations on the representatives of the main evolutionary groups show that their ecology is also different: the Central lineage is a mesophilic and cold-resistant form, while the other two closely related lineages are more xerophilic and thermophilic. Results of the potential ranges modeling and ecological niche analysis confirm that the genetic lineages occupy different niches of the Crimea. Furthermore, the area of inhabitation of the Central lineage splits the western and eastern parts of the Common lineage range, while the Southwestern lineage is restricted along the coast of the southwestern coast of the peninsula. The long-term co-existence of deeply divergent sister mitochondrial lineages in a relatively small (circa 7,000 km<sup>2</sup>) isolated mountain system serves as a mesocosm for understanding the speciation process. Our data suggest that the Central lineage warrants further taxonomic investigation.

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Becking, Leontine E., Christiaan A. de Leeuw, Bram Knegt, et al. "Highly divergent mussel lineages in isolated Indonesian marine lakes." PeerJ 4 (October 13, 2016): e2496. http://dx.doi.org/10.7717/peerj.2496.

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Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the musselBrachidontesfrom marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations ofBrachidontesspp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted fromin situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago.

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Yang, Yau-Wen, Pai-Yean Tai, and Ying Chen. "053 The Origin of Raphanus sativus Based on the DNA Sequences from Different Organelles." HortScience 35, no. 3 (2000): 397D—397. http://dx.doi.org/10.21273/hortsci.35.3.397d.

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There are two evolutionary pathways in the genus of Brassica, one is rapa/oleracea lineage and the other is nigra lineage. Based on the morphological characteristics and nuclear RAPD or RFLP markers, genus Raphanus was thought more closely related to nigra lineage than to rapa/oleracea lineage (Song et al., 1990; Thormann et al., 1994). RFLP data of both chloroplast and mitochondria revealed that Raphanus is more closely related to rapa/oleracea lineage (Palmer and Herbon, 1988; Warwick and Black, 1991; Pradhan et al., 1992). We have previously demonstrated that Raphanus sativus is more closely related to nigra lineage using nuclear intergenic spacer between 5S rDNA and internal transcribed spacer region between 18S and 25S rDNA. In this study, we analyzed DNA sequences from different regions of chloroplast and showed that Raphanus sativus was closely related to rapa/oleracea lineage than to nigra lineage. These results suggest that Raphanus sativus is a hybrid between B. rapa/oleracea and B nigra lineages as proposed by Song et al (1990). The split time between these two lineages and the divergent time of Raphanus was also determined based on these chloroplast DNA sequences.

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Jacobs, David S., Hassan Babiker, Anna Bastian, et al. "Phenotypic Convergence in Genetically Distinct Lineages of a Rhinolophus Species Complex (Mammalia, Chiroptera)." PLoS ONE 8, no. 12 (2013): e82614. https://doi.org/10.5281/zenodo.14819911.

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(Uploaded by Plazi for the Bat Literature Project) Phenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi, in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R. d. damarensis, should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi, suggesting that biological constraints are unlikely to have influenced the convergence. Instead, the striking similarity in morphology and sensory biology are probably the result of neutral evolutionary processes, resulting in the independent evolution of similar phenotypes.

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Ma, Tao, Kun Wang, Quanjun Hu, et al. "Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex." Proceedings of the National Academy of Sciences 115, no. 2 (2017): E236—E243. http://dx.doi.org/10.1073/pnas.1713288114.

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How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

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Hilgers, Leon, Stefanie Hartmann, Jobst Pfaender, et al. "Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails." Genes 13, no. 6 (2022): 1029. http://dx.doi.org/10.3390/genes13061029.

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(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.

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Liebeke, Manuel, Michael W. Bruford, Robert K. Donnelly, et al. "Identifying biochemical phenotypic differences between cryptic species." Biology Letters 10, no. 9 (2014): 20140615. http://dx.doi.org/10.1098/rsbl.2014.0615.

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Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus . There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as N ε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.

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Brown, Jeffrey G. "Ticks, Hair Loss, and Non-Clinging Babies: A Novel Tick-Based Hypothesis for the Evolutionary Divergence of Humans and Chimpanzees." Life 11, no. 5 (2021): 435. http://dx.doi.org/10.3390/life11050435.

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Human straight-legged bipedalism represents one of the earliest events in the evolutionary split between humans (Homo spp.) and chimpanzees (Pan spp.), although its selective basis is a mystery. A carrying-related hypothesis has recently been proposed in which hair loss within the hominin lineage resulted in the inability of babies to cling to their mothers, requiring mothers to walk upright to carry their babies. However, a question remains for this model: what drove the hair loss that resulted in upright walking? Observers since Darwin have suggested that hair loss in humans may represent an evolutionary strategy for defence against ticks. The aim of this review is to propose and evaluate a novel tick-based evolutionary hypothesis wherein forest fragmentation in hominin paleoenvironments created conditions that were favourable for tick proliferation, selecting for hair loss in hominins and grooming behaviour in chimpanzees as divergent anti-tick strategies. It is argued that these divergent anti-tick strategies resulted in different methods for carrying babies, driving the locomotor divergence of humans and chimpanzees.

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Cooper, Jacob C. "Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage." PeerJ 12 (April 30, 2024): e17345. http://dx.doi.org/10.7717/peerj.17345.

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Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species’ evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

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Rothstein, Andrew P., Allison Q. Byrne, Roland A. Knapp, et al. "Divergent regional evolutionary histories of a devastating global amphibian pathogen." Proceedings of the Royal Society B: Biological Sciences 288, no. 1953 (2021): 20210782. http://dx.doi.org/10.1098/rspb.2021.0782.

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Emerging infectious diseases are a pressing threat to global biological diversity. Increased incidence and severity of novel pathogens underscores the need for methodological advances to understand pathogen emergence and spread. Here, we use genetic epidemiology to test, and challenge, key hypotheses about a devastating zoonotic disease impacting amphibians globally. Using an amplicon-based sequencing method and non-invasive samples we retrospectively explore the history of the fungal pathogen Batrachochytrium dendrobatidis ( Bd ) in two emblematic amphibian systems: the Sierra Nevada of California and Central Panama. The hypothesis in both regions is the hypervirulent Global Panzootic Lineage of Bd ( Bd GPL) was recently introduced and spread rapidly in a wave-like pattern. Our data challenge this hypothesis by demonstrating similar epizootic signatures can have radically different underlying evolutionary histories. In Central Panama, our genetic data confirm a recent and rapid pathogen spread. However, Bd GPL in the Sierra Nevada has remarkable spatial structuring, high genetic diversity and a relatively older history inferred from time-dated phylogenies. Thus, this deadly pathogen lineage may have a longer history in some regions than assumed, providing insights into its origin and spread. Overall, our results highlight the importance of integrating observed wildlife die-offs with genetic data to more accurately reconstruct pathogen outbreaks.

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Vijayakumar, S. P., Riya C. Menezes, Aditi Jayarajan, and Kartik Shanker. "Glaciations, gradients, and geography: multiple drivers of diversification of bush frogs in the Western Ghats Escarpment." Proceedings of the Royal Society B: Biological Sciences 283, no. 1836 (2016): 20161011. http://dx.doi.org/10.1098/rspb.2016.1011.

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The historical processes underlying high diversity in tropical biodiversity hotspots like the Western Ghats of Peninsular India remain poorly understood. We sampled bush frogs on 13 massifs across the Western Ghats Escarpment and examined the relative influence of Quaternary glaciations, ecological gradients and geological processes on the spatial patterns of lineage and clade diversification. The results reveal a large in situ radiation (more than 60 lineages), exhibiting geographical structure and clade-level endemism, with two deeply divergent sister clades, North and South, highlighting the biogeographic significance of an ancient valley, the Palghat Gap. A majority of the bush frog sister lineages were isolated on adjacent massifs, and signatures of range stasis provide support for the dominance of geological processes in allopatric speciation. In situ diversification events within the montane zones (more than 1800 m) of the two highest massifs suggest a role for climate-mediated forest-grassland persistence. Independent transitions along elevational gradients among sub-clades during the Miocene point to diversification along the elevational gradient. The study highlights the evolutionary significance of massifs in the Western Ghats with the high elevations acting as centres of lineage diversification and the low- and mid-elevations of the southern regions, with deeply divergent lineages, serving as museums.

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Arrigo, Nicole C., A. Paige Adams, and Scott C. Weaver. "Evolutionary Patterns of Eastern Equine Encephalitis Virus in North versus South America Suggest Ecological Differences and Taxonomic Revision." Journal of Virology 84, no. 2 (2009): 1014–25. http://dx.doi.org/10.1128/jvi.01586-09.

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ABSTRACT The eastern equine encephalitis (EEE) complex consists of four distinct genetic lineages: one that circulates in North America (NA EEEV) and the Caribbean and three that circulate in Central and South America (SA EEEV). Differences in their geographic, pathogenic, and epidemiologic profiles prompted evaluation of their genetic diversity and evolutionary histories. The structural polyprotein open reading frames of all available SA EEEV and recent NA EEEV isolates were sequenced and used in evolutionary and phylogenetic analyses. The nucleotide substitution rate per year for SA EEEV (1.2 × 10−4) was lower and more consistent than that for NA EEEV (2.7 × 10−4), which exhibited considerable rate variation among constituent clades. Estimates of time since divergence varied widely depending upon the sequences used, with NA and SA EEEV diverging ca. 922 to 4,856 years ago and the two main SA EEEV lineages diverging ca. 577 to 2,927 years ago. The single, monophyletic NA EEEV lineage exhibited mainly temporally associated relationships and was highly conserved throughout its geographic range. In contrast, SA EEEV comprised three divergent lineages, two consisting of highly conserved geographic groupings that completely lacked temporal associations. A phylogenetic comparison of SA EEEV and Venezuelan equine encephalitis viruses (VEEV) demonstrated similar genetic and evolutionary patterns, consistent with the well-documented use of mammalian reservoir hosts by VEEV. Our results emphasize the evolutionary and genetic divergences between members of the NA and SA EEEV lineages, consistent with major differences in pathogenicity and ecology, and propose that NA and SA EEEV be reclassified as distinct species in the EEE complex.

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Fournier, Gregory P., Jinling Huang, and J. Peter Gogarten. "Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1527 (2009): 2229–39. http://dx.doi.org/10.1098/rstb.2009.0033.

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Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

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Jacquat, Andrés Gustavo, Martín Gustavo Theumer, and José Sebastián Dambolena. "Putative Mitoviruses without In-Frame UGA(W) Codons: Evolutionary Implications." Viruses 15, no. 2 (2023): 340. http://dx.doi.org/10.3390/v15020340.

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Mitoviruses are small vertically transmitted RNA viruses found in fungi, plants and animals. Taxonomically, a total of 105 species and 4 genera have been formally recognized by ICTV, and recently, 18 new putative species have been included in a new proposed genus. Transcriptomic and metatranscriptomic studies are a major source of countless new virus-like sequences that are continually being added to open databases and these may be good sources for identifying new putative mitoviruses. The search for mitovirus-like sequences in the NCBI databases resulted in the discovery of more than one hundred new putative mitoviruses, with important implications for taxonomy and also for the evolutionary scenario. Here, we propose the inclusion of four new putative members to the genus Kvaramitovirus, and the existence of a new large basally divergent lineage composed of 144 members that lack internal UGA codons (subfamily “Arkeomitovirinae”), a feature not shared by the vast majority of mitoviruses. Finally, a taxonomic categorization proposal and a detailed description of the evolutionary history of mitoviruses were carried out. This in silico study supports the hypothesis of the existence of a basally divergent lineage that could have had an impact on the early evolutionary history of mitoviruses.

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Moran, Paul, David J. Teel, Michael A. Banks, et al. "Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography." Canadian Journal of Fisheries and Aquatic Sciences 70, no. 3 (2013): 415–35. http://dx.doi.org/10.1139/cjfas-2012-0135.

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The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of life-history segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved — essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.

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Dunwell, Thomas L., Jordi Paps, and Peter W. H. Holland. "Novel and divergent genes in the evolution of placental mammals." Proceedings of the Royal Society B: Biological Sciences 284, no. 1864 (2017): 20171357. http://dx.doi.org/10.1098/rspb.2017.1357.

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Analysis of genome sequences within a phylogenetic context can give insight into the mode and tempo of gene and protein evolution, including inference of gene ages. This can reveal whether new genes arose on particular evolutionary lineages and were recruited for new functional roles. Here, we apply MCL clustering with all-versus-all reciprocal BLASTP to identify and phylogenetically date ‘Homology Groups’ among vertebrate proteins. Homology Groups include new genes and highly divergent duplicate genes. Focusing on the origin of the placental mammals within the Eutheria, we identify 357 novel Homology Groups that arose on the stem lineage of Placentalia, 87 of which are deduced to play core roles in mammalian biology as judged by extensive retention in evolution. We find the human homologues of novel eutherian genes are enriched for expression in preimplantation embryo, brain, and testes, and enriched for functions in keratinization, reproductive development, and the immune system.

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McVay, John D., Duncan Hauser, Andrew L. Hipp, and Paul S. Manos. "Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America." Genome 60, no. 9 (2017): 733–42. http://dx.doi.org/10.1139/gen-2016-0206.

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Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.

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Mahmoudi, Ahmad, Lutz C. Maul, Masoumeh Khoshyar, Jamshid Darvish, Mansour Aliabadian, and Boris Kryštufek. "Evolutionary history of water voles revisited: confronting a new phylogenetic model from molecular data with the fossil record." Mammalia 84, no. 2 (2020): 171–84. http://dx.doi.org/10.1515/mammalia-2018-0178.

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AbstractRecent water voles (genus Arvicola) display a prominent morphological diversity with a strong ecotypical background but with unclear taxonomic associations. We provide a novel synthetic view on the evolutionary history and the current taxonomic richness in the genus. Our molecular reconstruction, based on a 1143-bp-long sequence of cytochrome b and a 926-bp interphotoreceptor retinoid binding protein (irbp) confirmed the monophyly of four species (amphibius, sapidus, monticola and italicus) recognized thus far, and retrieved a new deeply divergent lineage from West Iran. Genetic divergence of the Iranian lineage (>9.0%) is inside the range of interspecies distances, exceeding the interspecies divergences between the remaining Arvicola species (range, 4.3–8.7%). The oldest name available for the Iranian phylogroup is Arvicola persicus de Filippi, 1865, with the type locality in Soltaniyeh, Iran. The molecular clock suggests the divergence of A. persicus in the Early Pleistocene (2.545 Ma), and the current radiation of the remaining species between 1.535 Ma (Arvicola sapidus) and 0.671 Ma. While A. sapidus possibly evolved from Arvicola jacobaeus, a fossil ancestor to A. persicus is unknown. The aquatic life-style of Mimomys savini, a direct ancestor to some fossil Arvicola, is retained in recent stem species A. sapidus and A. persicus, while a major shift toward fossorial morphotype characterizes the terminal lineages (amphibius, italicus and monticola). We suggest that habitat-dependent morphological plasticity and positive enamel differentiation in Arvicola amphibius widened its ecological niche that might trigger a range expansion across c. 12 million km2, making it one of the largest among arvicolines.

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Dewals, Benjamin, Muriel Thirion, Nicolas Markine-Goriaynoff, et al. "Evolution of Bovine herpesvirus 4: recombination and transmission between African buffalo and cattle." Journal of General Virology 87, no. 6 (2006): 1509–19. http://dx.doi.org/10.1099/vir.0.81757-0.

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Bovine herpesvirus 4 (BoHV-4) has been isolated from cattle throughout the world, but virological and serological studies have suggested that the African buffalo is also a natural host for this virus. It has previously been found that the Bo17 gene of BoHV-4 was acquired from an ancestor of the African buffalo, probably around 1.5 million years ago. Analysis of the variation of the Bo17 gene sequence among BoHV-4 strains suggested a relatively ancient transmission of BoHV-4 from the buffalo to the Bos primigenius lineage, followed by a host-dependent split between zebu and taurine BoHV-4 strains. In the present study, the evolutionary history of BoHV-4 was investigated by analysis of five gene sequences from each of nine strains representative of the viral species: three isolated from African buffalo in Kenya and six from cattle from Europe, North America and India. No two gene sequences had the same evolutionary tree, indicating that recombination has occurred between divergent lineages; six recombination events were delineated for these sequences. Nevertheless, exchange has been infrequent enough that a clonal evolutionary history of the strains could be discerned, upon which the recombination events were superimposed. The dates of divergence among BoHV-4 lineages were estimated from synonymous nucleotide-substitution rates. The inferred evolutionary history suggests that African buffalo were the original natural reservoir of BoHV-4 and that there have been at least three independent transmissions from buffalo to cattle, probably via intermediate hosts and – at least in the case of North American strains – within the last 500 years.

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Han, Shiyun, Hengwu Ding, De Bi, et al. "Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales." Plants 11, no. 24 (2022): 3544. http://dx.doi.org/10.3390/plants11243544.

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As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.

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Mullen, Sean P., Nicholas W. VanKuren, Wei Zhang, et al. "Disentangling Population History and Character Evolution among Hybridizing Lineages." Molecular Biology and Evolution 37, no. 5 (2020): 1295–305. http://dx.doi.org/10.1093/molbev/msaa004.

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Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

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Liu, Yantao, Long Hou, Liqin Liu, Amna Sulaman, and Faiz Muhammad. "Mitochondrial DNA reveals two recent diverged lineages in Amphioctopus aegina (Gray, 1849) (Cephalopoda, Octopodidae) across the Leizhou Peninsula: a marine ecoregion barrier." ZooKeys 1179 (September 14, 2023): 299–311. http://dx.doi.org/10.3897/zookeys.1179.96015.

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Amphioctopus aegina is an economically important species that has been intensively exploited in the marine areas along the Chinese coast. However, the genetic variation and population genetic structure, which would provide valuable information for their fisheries management, have rarely been investigated. In this study, the genetic variation within and among four A. aegina populations throughout its full distribution range were estimated based on mitochondrial cytochrome b DNA sequences. Our results indicated low (Qinzhou) to high (Dongshan) genetic diversities among the four populations. Analysis of molecular variance (AMOVA), ΦST statistics, phylogenetic tree and haplotype networks revealed two significant (p &lt; 0.01) divergent lineages with a ΦST value of 0.7116 between them, one from a population in Qinzhou and the other from the remaining three populations of Dongshan, Huizhou and Zhanjiang. However, the low genetic distance (0.0032) and only two fixed substitutions between them suggest their recent divergence is possibly due to the last glacial period barriers to gene flow produced by the Leizhou Peninsula. The observed lineage divergence suggests that populations of A. aegina in China are genetically subdivided and may represent evolutionary lineages that should be managed individually.

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Amphioctopus aegina is an economically important species that has been intensively exploited in the marine areas along the Chinese coast. However, the genetic variation and population genetic structure, which would provide valuable information for their fisheries management, have rarely been investigated. In this study, the genetic variation within and among four A. aegina populations throughout its full distribution range were estimated based on mitochondrial cytochrome b DNA sequences. Our results indicated low (Qinzhou) to high (Dongshan) genetic diversities among the four populations. Analysis of molecular variance (AMOVA), ΦST statistics, phylogenetic tree and haplotype networks revealed two significant (p < 0.01) divergent lineages with a ΦST value of 0.7116 between them, one from a population in Qinzhou and the other from the remaining three populations of Dongshan, Huizhou and Zhanjiang. However, the low genetic distance (0.0032) and only two fixed substitutions between them suggest their recent divergence is possibly due to the last glacial period barriers to gene flow produced by the Leizhou Peninsula. The observed lineage divergence suggests that populations of A. aegina in China are genetically subdivided and may represent evolutionary lineages that should be managed individually.

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Anderson, Sean A. S., and Jason T. Weir. "Character displacement drives trait divergence in a continental fauna." Proceedings of the National Academy of Sciences 118, no. 20 (2021): e2021209118. http://dx.doi.org/10.1073/pnas.2021209118.

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Coexisting (sympatric) pairs of closely related species are often characterized by exaggerated trait differences. This widespread pattern is consistent with adaptation for reduced similarity due to costly interactions (i.e., “character displacement”)—a classic hypothesis in evolutionary theory. But it is equally consistent with a community assembly bias in which lineages with greater trait differences are more likely to establish overlapping ranges in the first place (i.e., “species sorting”), as well as with null expectations of trait divergence through time. Few comparative analyses have explicitly modeled these alternatives, and it remains unclear whether trait divergence is a general prerequisite for sympatry or a consequence of interactions between sympatric species. Here, we develop statistical models that allow us to distinguish the signature of these processes based on patterns of trait divergence in closely related lineage pairs. We compare support for each model using a dataset of bill shape differences in 207 pairs of New World terrestrial birds representing 30 avian families. We find that character displacement models are overwhelmingly supported over species sorting and null expectations, indicating that exaggerated bill shape differences in sympatric pairs result from enhanced divergent selection in sympatry. We additionally detect a latitudinal gradient in character displacement, which appears strongest in the tropics. Our analysis implicates costly species interactions as powerful drivers of trait divergence in a major vertebrate fauna. These results help substantiate a long-standing but equivocally supported linchpin of evolutionary theory.

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Byrne, M. "Phylogeography provides an evolutionary context for the conservation of a diverse and ancient flora." Australian Journal of Botany 55, no. 3 (2007): 316. http://dx.doi.org/10.1071/bt06072.

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Phylogeography can inform conservation strategies through assessment of genetic diversity that incorporates an evolutionary perspective, and allows evaluation within a geographical context, thus providing integration with other biogeographical information. Comparative phylogeography can identify significant historical processes that have had major influences on the biota and provides a historical context for understanding current species distributions. The phylogeographic patterns in the flora of south-western Australia are reviewed. Concordant patterns of lineage divergence in three unrelated taxa from separate families with widespread distributions indicate a common response to major historical processes involved in Pleistocene climatic fluctuations. Identification of highly divergent haplotypes in some species indicates areas that may represent refugia during times of climatic instability. Analysis of phylogeographic patterns in the flora of south-western Australia has revealed the influence of historical climate change in promoting high phylogenetic diversity within species that is comparable to the high species diversity that is well known in the Western Australian flora. Knowledge of historical influences and species responses provides an evolutionary context for conservation management strategies that facilitate the continued action of dynamic evolutionary processes.

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Peña, Tomas A., Pablo Villarreal, Nicolas Agier, et al. "An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia." PLOS Genetics 20, no. 9 (2024): e1011396. http://dx.doi.org/10.1371/journal.pgen.1011396.

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Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct Saccharomyces lineage in Nothofagus forests of coastal Patagonia. This lineage, designated Saccharomyces chiloensis sp. nov., exhibits 7% genetic divergence from its sister species S. uvarum, as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent S. uvarum population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to S. uvarum, which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from S. uvarum. In addition, we found unique structural variants between S. chiloensis sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that S. chiloensis sp. nov diverged from S. uvarum in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of S. chiloensis sp. nov. illustrates the uniqueness of Patagonia’s coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of S. chiloensis sp. nov. is CBS 18620T.

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Schield, Drew R., Blair W. Perry, Richard H. Adams, et al. "Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation." Biological Journal of the Linnean Society 128, no. 1 (2019): 149–69. http://dx.doi.org/10.1093/biolinnean/blz077.

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Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.

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Wei, Kai, Tingting Zhang, and Lei Ma. "Divergent and convergent evolution of housekeeping genes in human–pig lineage." PeerJ 6 (May 24, 2018): e4840. http://dx.doi.org/10.7717/peerj.4840.

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Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

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Tarr, Cheryl L., and Thomas S. Whittam. "Molecular Evolution of the Intimin Gene in O111 Clones of Pathogenic Escherichia coli." Journal of Bacteriology 184, no. 2 (2002): 479–87. http://dx.doi.org/10.1128/jb.184.2.479-487.2002.

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ABSTRACT Intimin is an important virulence factor in two groups of enteric pathogens: enteropathogenic Escherichia coli (EPEC), which is a major cause of infant diarrhea in the developing world, and enterohemorrhagic E. coli (EHEC), which has caused large food-borne outbreaks of hemorrhagic colitis in the United States and other developed countries. Intimin is encoded on a 35-kb pathogenicity island called the locus of enterocyte effacement (LEE). At least five antigenic types have been described for the highly variable gene, and each type is generally characteristic of particular evolutionary lineages. We determined the nucleotide sequences of intimin and other LEE genes in two O111 clones that have not been amenable to typing. The sequences from both O111:H8 and O111:H9 differed from the Int-β that is typical of other clones in the same evolutionary lineage. The sequence from the O111:H8 strains was a mosaic of divergent segments that alternately clustered with Int-α, Int-β, or Int-γ. The sequence from the O111:H9 clone consistently showed a close relationship with that from E2348/69, a distantly related strain that expresses Int-α. The results suggest that there have been multiple acquisitions of the LEE in the EHEC 2/EPEC 2 clonal lineage, with a recent turnover in either O111:H8 or its close relatives. Amino acid substitutions that alter residue charge occurred more frequently than would be expected under random substitution in the extracellular domains of intimin, suggesting that diversifying selection has promoted divergence in this region of the protein. An N-terminal domain that presumably functions in the periplasm may also be under positive selection.

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Bond, Jason E., David A. Beamer, Marshal C. Hedin, and Petra Sierwald. "Gradual evolution of male genitalia in a sibling species complex of millipedes (Diplopoda : Spirobolida : Rhinocricidae : Anadenobolus)." Invertebrate Systematics 17, no. 6 (2003): 711. http://dx.doi.org/10.1071/is03026.

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Jamaican millipedes in the Anadenobolus species complex provide an unusual case study of arthropods having undergone speciation in the absence of conspicuous divergence of male genitalia. Using landmark-based morphometrics, we examined shape deformation of the male anterior copulatory device in three genetically divergent yet morphologically cryptic species. A multivariate analysis of variance and relative warp analysis of nonuniform components show that although male genitalic shape is statistically different among species, many specimens are 'misplaced' in morphological space, perhaps consistent with a condition analogous to incomplete lineage sorting. A simulation of neutral nuclear gene coalescence suggests that such incomplete sorting is expected, given the depth of mtDNA divergences observed across species. The pronounced contrast between deep molecular v. incomplete genitalic divergence is at odds with the paradigm of selection-driven rapid change in male copulatory structure during arthropod speciation. Alternatively, we suggest that male genitalic divergence is evolving neutrally or in concert with other components of the genome (pleiotropy). Although we recognise the empirical validity of rapid genitalic divergence via sexual selection or sexual conflict, such models must be empirically tested using multiple lines of evidence. Accepting the rapid and divergent hypothesis without such multiple evidence scrutiny may result in a gross underestimation of evolutionary diversity and, subsequently, the misinterpretation of processes shaping genitalic change.

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Mira, Francesco, Marta Canuti, Giuseppa Purpari, et al. "Molecular Characterization and Evolutionary Analyses of Carnivore Protoparvovirus 1 NS1 Gene." Viruses 11, no. 4 (2019): 308. http://dx.doi.org/10.3390/v11040308.

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Carnivore protoparvovirus 1 is the etiological agent of a severe disease of terrestrial carnivores. This unique specie encompasses canine parvovirus type 2 (CPV-2) and feline panleukopenia virus (FPLV). Studies widely analyzed the main capsid protein (VP2), but limited information is available on the nonstructural genes (NS1/NS2). This paper analyzed the NS1 gene sequence of FPLV and CPV strains collected in Italy in 2009–2017, along with worldwide related sequences. Differently from VP2, only one NS1 amino-acid residue (248) clearly and constantly distinguished FPLV from CPV-2, while five possible convergent amino-acid changes were observed that may affect the functional domains of the NS1. Some synonymous mutation in NS1 were non-synonymous in NS2 and vice versa. No evidence for recombination between the two lineages was found, and the predominance of negative selection pressure on NS1 proteins was observed, with low and no overlap between the two lineages in negatively and positively selected codons, respectively. More sites were under selection in the CPV-2 lineage. NS1 phylogenetic analysis showed divergent evolution between FPLV and CPV, and strains were clustered mostly by country and year of detection. We highlight the importance of obtaining the NS1/NS2 coding sequence in molecular epidemiology investigations.

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Løken, S. B., I. Skrede, and T. Schumacher. "The Helvella corium species aggregate in Nordic countries – phylogeny and species delimitation." Fungal Systematics and Evolution 5, no. 1 (2020): 169–86. http://dx.doi.org/10.3114/fuse.2020.05.11.

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Mycologists have always been curious about the elaborate morphotypes and shapes of species of the genus Helvella. The small, black, cupulate Helvella specimens have mostly been assigned to Helvella corium, a broadly defined morpho-species. Recent phylogenetic analyses, however, have revealed an aggregate of species hidden under this name. We performed a multispecies coalescent analysis to re-assess species limits and evolutionary relationships of the Helvella corium species aggregate in the Nordic countries. To achieve this, we used morphology and phylogenetic evidence from five loci – heat shock protein 90 (hsp), translation elongation factor 1-alpha (tef), RNA polymerase II (rpb2), and the 5.8S and large subunit (LSU) of the nuclear ribosomal DNA. All specimens under the name Helvella corium in the larger university fungaria of Norway, Sweden and Denmark were examined and barcoded, using partial hsp and/or rpb2 as the preferential secondary barcodes in Helvella. Additional fresh specimens were collected in three years (2015–2018) to obtain in vivo morphological data to aid in species discrimination. The H. corium species aggregate consists of seven phylogenetically distinct species, nested in three divergent lineages, i.e. H. corium, H. alpina and H. pseudoalpina sp. nov. in the /alpina-corium lineage, H. alpestris, H. macrosperma and H. nannfeldtii in the /alpestris-nannfeldtii lineage, and H. alpicola as a weakly supported sister to the /alpestris-nannfeldtii lineage. Among the seven species, the ribosomal loci expressed substantial variation in evolutionary rates, suggesting care in the use of these regions alone in delimitation of Helvella species. Altogether, 469 out of 496 available fungarium specimens were successfully barcoded.

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Setiamarga, Davin H. E., Masaki Miya, Yusuke Yamanoue, et al. "Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates." Biology Letters 5, no. 6 (2009): 812–16. http://dx.doi.org/10.1098/rsbl.2009.0419.

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The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

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Muñoz-Gómez, Sergio A., Shannon N. Snyder, Samantha J. Montoya, and Jeremy G. Wideman. "Independent accretion of TIM22 complex subunits in the animal and fungal lineages." F1000Research 9 (August 28, 2020): 1060. http://dx.doi.org/10.12688/f1000research.25904.1.

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Background: The mitochondrial protein import complexes arose early in eukaryogenesis. Most of the components of the protein import pathways predate the last eukaryotic common ancestor. For example, the carrier-insertase TIM22 complex comprises the widely conserved Tim22 channel core. However, the auxiliary components of fungal and animal TIM22 complexes are exceptions to this ancient conservation. Methods: Using comparative genomics and phylogenetic approaches, we identified precisely when each TIM22 accretion occurred. Results: In animals, we demonstrate that Tim29 and Tim10b arose early in the holozoan lineage. Tim29 predates the metazoan lineage being present in the animal sister lineages, choanoflagellate and filastereans, whereas the erroneously named Tim10b arose from a duplication of Tim9 at the base of metazoans. In fungi, we show that Tim54 has representatives present in every holomycotan lineage including microsporidians and fonticulids, whereas Tim18 and Tim12 appeared much later in fungal evolution. Specifically, Tim18 and Tim12 arose from duplications of Sdh3 and Tim10, respectively, early in the Saccharomycotina. Surprisingly, we show that Tim54 is distantly related to AGK suggesting that AGK and Tim54 are extremely divergent orthologues and the origin of AGK/Tim54 interaction with Tim22 predates the divergence of animals and fungi. Conclusions: We argue that the evolutionary history of the TIM22 complex is best understood as the neutral structural divergence of an otherwise strongly functionally conserved protein complex. This view suggests that many of the differences in structure/subunit composition of multi-protein complexes are non-adaptive. Instead, most of the phylogenetic variation of functionally conserved molecular machines, which have been under stable selective pressures for vast phylogenetic spans, such as the TIM22 complex, is most likely the outcome of the interplay of random genetic drift and mutation pressure.

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Collins, Catherine J., Nicolas J. Rawlence, Stefan Prost, et al. "Extinction and recolonization of coastal megafauna following human arrival in New Zealand." Proceedings of the Royal Society B: Biological Sciences 281, no. 1786 (2014): 20140097. http://dx.doi.org/10.1098/rspb.2014.0097.

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Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage ( Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction–replacement event in penguins ( Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.

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Min, Jimin, Guangsheng Pei, Vittorio Branchi, et al. "Abstract PR08: Spatial mapping of transcriptomic and lineage diversity in metastatic pancreatic cancer." Cancer Research 84, no. 2_Supplement (2024): PR08. http://dx.doi.org/10.1158/1538-7445.panca2023-pr08.

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Abstract Patients with treatment refractory pancreatic ductal adenocarcinoma (PDAC) often succumb to widespread systemic metastases; however, the current understanding of transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied. Here we constructed high-resolution maps of clonal architecture and lineage states using spatially resolved transcriptomic profiles from 13 primary PDAC and corresponding liver, lung, and peritoneal metastases (total of 49 sites), using samples obtained from the UNMC Rapid Autopsy Program (RAP). We demonstrate discernible transcriptomic shifts, with the most pronounced distinctions between liver and lung loci, and fluctuations in the expression of basal and classical markers during the transition from primary tumor to organ-specific metastases. Through inferring copy number variations, we revealed clonal heterogeneity within both primary tumors and metastases and the diversity of spatial clonal distributions. Construction of phylogenetic trees facilitated the mapping of patient-specific clonal hierarchies and a variety of evolutionary trajectories. These included five discrete evolutionary modes within primary tumors and selective clonal expansions in divergent spatial regions of metastases, even within the same organ site, particularly notable in the liver. We identified the coexistence of multiple tumor lineages within each tissue and observed site-specific lineage plasticity. Lung metastases presented a marked lineage transition, while liver and peritoneal metastases frequently reflected the lineage composition of the primary tumor. Two metastatic loci within the liver demonstrated spatial divergence in tumor lineages within the same organ site. Comparative transcriptomic analysis with the imputation of super-resolution gene expression revealed that tumor regions in an intermediate state, a bi-phenotypic status bridging basal and classical subtypes, harbored a potent immunogenic gene expression signature and antigen-presenting cancer-associated fibroblasts (CAFs). We noted a unique distribution of myofibroblastic CAFs (myCAFs) and angiogenesis-related tumor-associated macrophages (TAMs) in the basal lineage tumor regions. While both cell populations were abundant within the basal lineage tumors, an increased presence of myCAFs was also observed in the tumor microenvironment (TME) juxta-tumoral to neoplastic cells. In the majority of tissues, irrespective of site and lineage, we observed an exclusion of plasma cells from the tumor bed and adjacent TME, areas where myCAFs with abundant TGFB1 expression are present. Strong CXCL12 expression co-localized with plasma cells, suggesting the potential for interstitial CAFs-induced plasma cell exclusion via CXCL12 in PDAC and its metastases. Collectively, our findings underscore the potential of spatial molecular state mapping to predict regional changes and corresponding TME dynamics. This insight holds promise for enabling personalized stratification of PDAC patients with multi-organ metastasis and for pioneering more effective therapeutic avenues. Citation Format: Jimin Min, Guangsheng Pei, Vittorio Branchi, Kimal I. Rajapakshe, Paul M. Grandgenett, Michael A. Hollingsworth, Paola A. Guerrero, Anirban Maitra, Linghua Wang. Spatial mapping of transcriptomic and lineage diversity in metastatic pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr PR08.

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Makhov, Ilia A., Yelizaveta Y. U. Gorodilova, and Vladimir A. Lukhtanov. "Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia?" Biological Journal of the Linnean Society 134, no. 2 (2021): 342–65. http://dx.doi.org/10.1093/biolinnean/blab089.

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Abstract The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.

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Hanna, Zachary R., Carla Cicero, and Rauri C. K. Bowie. "Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage." PeerJ 7 (August 6, 2019): e7388. http://dx.doi.org/10.7717/peerj.7388.

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We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.

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McKee, Clifton D., David T. S. Hayman, Michael Y. Kosoy, and Colleen T. Webb. "Phylogenetic and geographic patterns of bartonella host shifts among bat species." Infection, Genetics and Evolution 44 (June 12, 2016): 382–94. https://doi.org/10.5281/zenodo.13530267.

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(Uploaded by Plazi for the Bat Literature Project) The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these methods to other infectious bacteria and viruses could uncover common processes that lead to parasite diversification and the formation of host-parasite relationships.

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McKee, Clifton D., David T. S. Hayman, Michael Y. Kosoy, and Colleen T. Webb. "Phylogenetic and geographic patterns of bartonella host shifts among bat species." Infection, Genetics and Evolution 44 (June 7, 2016): 382–94. https://doi.org/10.5281/zenodo.13530267.

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Malekian, Mansoureh, Steven J. B. Cooper, and Susan M. Carthew. "Phylogeography of the Australian sugar glider (Petaurus breviceps): evidence for a new divergent lineage in eastern Australia." Australian Journal of Zoology 58, no. 3 (2010): 165. http://dx.doi.org/10.1071/zo10016.

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The sugar glider (Petaurus breviceps) shows considerable variation in external morphology and mitochondrial DNA (mtDNA) diversity across its distribution in New Guinea and Australia. Here we investigate the phylogeography of P. breviceps in Australia using data from two mitochondrial genes (ND2 and ND4) and a nuclear gene (ω-globin). Phylogenetic analyses revealed the existence of two divergent mtDNA clades that are distributed over distinct geographical regions, one from coastal New South Wales and south-eastern Queensland and a second over the remaining distributional range of the species in Australia. The two groups generally had distinct ω-globin haplotypes that differed by one or two mutational steps. Analyses of Molecular Variation further supported the presence of at least two populations, accounting for 84.8% of the total mtDNA variation and 44% of the ω-globin variation. The general concordance of phylogeographic and population analyses suggests that population subdivision, possibly resulting from the combined influences of aridification after the Pliocene and uplift of the Great Dividing Range has impacted the evolution of P. breviceps. Our results also show that the geographical distribution of the two evolutionary lineages does not correspond with the distribution of the current morphological subspecies and we further propose that they be considered as separate Evolutionarily Significant Units for the purposes of conservation management.

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