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1. Molecular phylogenetic estimates of evolutionary affinities and the first reports of phenotypic variation in two secretive, endemic reptiles from the Romblon Island Group, central Philippines) from Luzon Island, the Philippines

   https://doi.org/10.26757/pjsb2020b14002  

   Meneses, C.G. (January 2020, Philippine Journal of Systematic Biology)

   null (Ed.)

   We report on the first molecular estimates of phylogenetic relationships of Brachymeles dalawangdaliri (Scincidae) and Pseudogekko isapa (Gekkonidae), and present new data on phenotypic variation in these two poorly known taxa, endemic to the Romblon Island Group of the central Philippines. Because both species were recently described on the basis of few, relatively older, museum specimens collected in the early 1970s (when preservation of genetic material was not yet standard practice in biodiversity field inventories), neither taxon has ever been included in modern molecular phylogenetic analyses. Likewise, because the original type series for each species consisted of only a few specimens, biologists have been unable to assess standard morphological variation in either taxon, or statistically assess the importance of characters contributing to their diagnoses and identification. Here we ameliorate both historical shortfalls. First, our new genetic data allowed us to perform novel molecular phylogenetic analyses aimed at elucidating the evolutionary relationships of these lineages; secondly, with population level phenotypic data, from the first statistical sample collected for either species, and including adults of both sexes. We reaffirm the distinctiveness of both named taxa as valid species, amend their diagnoses to facilitate the recognition of both, distinguish them from congeners, and consider the biogeographic affinities of both lineages. Our contribution emphasizes the conservation significance of Sibuyan Island’s Mt. Guiting-Guiting Natural Park, the diverse, idiosyncratic biogeographic histories of its variably-assembled, highly endemic reptile fauna, and the critical importance of multiple, repeated, survey–resurvey studies for understanding forest community species composition and the evolutionary history of Philippine biodiversity. 

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2. Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera: Formicidae), a Mesoamerican Ant Clade

   https://doi.org/10.1093/isd/ixab025  

   Ward, Philip S.; Branstetter, Michael G.; Sosa-Calvo, ed., Jeffrey (January 2022, Insect Systematics and Diversity)

   Abstract Using genetic, morphological, and geographical evidence, we investigate the species-level taxonomy and evolutionary history of the Pseudomyrmex elongatulus group, a clade of ants distributed from southwestern United States to Costa Rica. Through targeted enrichment of 2,524 UCE (ultraconserved element) loci we generate a phylogenomic data set and clarify the phylogenetic relationships and biogeographic history of these ants. The crown group is estimated to have originated ~8 Ma, in Mexico and/or northern Central America, and subsequently expanded into southern Central America and the southwestern Nearctic. The P. elongatulus group contains a mix of low- and high-elevation species, and there were apparently multiple transitions between these habitat types. We uncover three examples of one species—of restricted or marginal geographical distribution—being embedded phylogenetically in another species, rendering the latter paraphyletic. One of these cases involves an apparent workerless social parasite that occurs sympatrically with its parent species, with the latter serving as host. This suggests a sympatric origin of the parasite species within the distribution range of its host. Species boundaries are tested using three molecular delimitation approaches (SODA, bPTP, BPP) but these methods generate inflated species estimates (26–46 species), evidently because of a failure to distinguish population structure from species differences. In a formal taxonomic revision of the P. elongatulus group, based on almost 3,000 specimens from ~625 localities, we allow for geographic variation within species and we employ distinctness-in-sympatry criteria for testing hypotheses about species limits. Under these guidelines we recognize 13 species, of which nine are new: P. arcanus, sp. nov. (western Mexico); P. capillatus, sp. nov. (western Mexico); P. cognatus, sp. nov. (Chiapas, Mexico to Nicaragua); P. comitator, sp. nov. (Chiapas, Mexico); P. ereptor, sp. nov. (Veracruz, Mexico); P. exoratus, sp. nov. (southeastern Mexico, Honduras); P. fasciatus, sp. nov. (Chiapas, Mexico to Costa Rica); P. nimbus, sp. nov. (Costa Rica); and P. veracruzensis, sp. nov. (Veracruz, Mexico). Our study highlights the value of combining phylogenomic, phenotypic, and geographical data to resolve taxonomic and evolutionary questions. 

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3. Evolutionary structure and timing of major habitat shifts in Crocodylomorpha

   https://doi.org/10.1038/s41598-018-36795-1  

   Wilberg, Eric W.; Turner, Alan H.; Brochu, Christopher A. (January 2019, Scientific Reports)

   Abstract Extant crocodylomorphs are semiaquatic ambush predators largely restricted to freshwater or estuarine environments, but the group is ancestrally terrestrial and inhabited a variety of ecosystems in the past. Despite its rich ecological history, little effort has focused on elucidating the historical pattern of ecological transitions in the group. Traditional views suggested a single shift from terrestrial to aquatic in the Early Jurassic. However, new fossil discoveries and phylogenetic analyses tend to imply a multiple-shift model. Here we estimate ancestral habitats across a comprehensive phylogeny and show at least three independent shifts from terrestrial to aquatic and numerous other habitat transitions. Neosuchians first invade freshwater habitats in the Jurassic, with up to four subsequent shifts into the marine realm. Thalattosuchians first appear in marine habitats in the Early Jurassic. Freshwater semiaquatic mahajangasuchids are derived from otherwise terrestrial notosuchians. Within nearly all marine groups, some species return to freshwater environments. Only twice have crocodylomorphs reverted from aquatic to terrestrial habitats, both within the crown group. All living non-alligatorid crocodylians have a keratinised tongue with salt-excreting glands, but the lack of osteological correlates for these adaptations complicates pinpointing their evolutionary origin or loss. Based on the pattern of transitions to the marine realm, our analysis suggests at least four independent origins of saltwater tolerance in Crocodylomorpha. 

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4. Biogeography and ecological drivers of evolution in the Andes: resolving the phylogenetic backbone for Calceolaria (Calceolariaceae)

   https://doi.org/10.1093/botlinnean/boab079  

   Frankel, Lauren; Murúa, Maureen; Espíndola, Anahí (February 2022, Botanical Journal of the Linnean Society)

   Abstract Calceolaria (Calceolariaceae) is an emblematic and diverse genus in the Americas. Despite being one of the most easily recognized genera in the region and a system with great potential to improve our understanding of different drivers of species diversification in the Andes, its intrageneric evolutionary relationships are still poorly understood. Responding to the need for additional molecular markers to resolve the phylogenetic relationships of the group, we perform plastome analyses and resolve the backbone of the genus. Specifically, using low-coverage genomes for 14 species, we assembled plastomes, estimated and dated phylogenetic hypotheses and evaluated evolutionary trends in the group. Our approach allowed us to resolve the backbone of the genus, identify two main clades and estimate a timing of diversification contemporaneous to major climatic and orogenic events. Our biogeographic reconstructions suggest an independent colonization of the whole range of the genus by both clades. Finally, our evaluations of floral morphology reveal future avenues for investigating the relationship between the pollination biology and diversification of the group. 

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5. An ultraconserved element probe set for velvet worms (Onychophora)

   https://doi.org/10.1016/j.ympev.2024.108115  

   Sato, Shoyo; Derkarabetian, Shahan; Lord, Arianna; Giribet, Gonzalo (August 2024, Molecular Phylogenetics and Evolution)

   Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families – Peripatopsidae and Peripatidae – and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ~ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics. 

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