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1. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

   KIN ONN CHAN, CARL R. ( January 2021 , Systematic biology)

   In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specificways in which gene flowcan cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. Wemore »demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-bydistance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.« less
2. Unexpectedly high levels of lineage diversity in Sundaland Puddle Frogs (Dicroglossidae: Occidozyga Kuhl and Van Hasselt, 1822).

   Flury, J. ( January 2021 , Molecular phylogenetics and evolution)

   One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world’s so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads tomore »the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace’s Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.« less
3. A new, morphologically cryptic species of fanged frog, genus Limnonectes (Amphibia: Anura: Dicroglossidae), from Mindoro Island, central Philippines.

   Mark W. Herr, Johana Goyes ( January 2021 , Copeia)

   We describe a new species of fanged frog (genus Limnonectes) from Mindoro and Semirara Islands, of the Mindoro Pleistocene Aggregate Island Complex, of the central Philippines. Although morphologically indistinguishable from its closest relative, Limnonectes acanthi, of the Palawan faunal region, the two species can be readily diagnosed on the basis of spectral (dominant frequency) and temporal (pulse number and structure) properties of their advertisement calls, and their allopatric insular geographic ranges on permanently separate geological platforms which have not been connected by dry land in the recent geological past—all of which we interpret as congruent and independent lines of evidence supporting our recognition of two independently evolving evolutionary lineages (species). Ribosomal RNA mitochondrial gene sequences were used to provide genetic identification of specimens and estimate phylogenetic relationships; genetic divergences between Palawan and Mindoro faunal regions exceed those estimated among other, uncontroversial, phenotypically distinct Philippine species with equivalent levels of allopatry and biogeographic isolation. The recognition of the new species further emphasizes the degree to which even well-studied Philippine landmasses still harbor unrecognized biodiversity, and suggests that other widespread Philippine fanged frogs should be scrutinized for non-traditional diagnostic character differences (mate-recognition signal divergence, ecological differences, larval characteristics, life-history trait variation), especiallymore »when their geographic ranges span the archipelago’s permanent, deep-water trenches, which define its well-characterized Pleistocene Aggregate Island Complexes« less
4. Volume 14 Issue 2 - 2020 | 1 © Association of Systematic Biologists of the Philippines Molecular systematic investigation of Philippine puddle frogs (Anura: Dicroglossidae: Occidozyga Kuhl and Van Hasselt, 1822) reveals new candidate species and a novel pattern of species dyads

   Kin Onn Chan, Sabine Schoppe ( January 2021 , Philippine journal of systematic biology)

   Focusing on the phylogenetic relationships of puddle frog populations spanning the biogeographic interface between Sundaland (Borneo) and the Philippines, we demonstrate, for the first time, a widespread geographic pattern involving the existence of multiple divergent and co-distributed (sympatric) evolutionary lineages, most of which are not each other’s closest relatives, and all of which we interpret as probable distinct species. This pattern of co-occurrence in the form of pairs of ecologically distinct puddle frog forms (dyads), prevails throughout northern Borneo, Palawan, Tawi-Tawi, the Sulu Archipelago, and western Mindanao (Zamboanga). Previously obscured by outdated taxonomy and logistical, legal, and security obstacles to field-based natural history studies, this pattern has remained hidden from biogeographers and amphibian biologists by an uncontested proposal that Philippine Occidozyga laevis is a single, “widespread,” and “highly variable” species. In this paper we use an integrative synthesis of new genetic data, organismal phenotypic data, historical literature reports, and ecological observations to elucidate an interesting and potentially widespread pattern of puddle frog species coexistence at the Sundaland–Philippine biogeographic interface. Calling attention to this pattern opens promising possibilities for future research aimed at understanding the scope of this dyads pattern, and whether it extends to the more northern reaches of themore »Philippines. On either side of Huxley’s and Wallace’s lines, data suggest that the majority of puddle frog dyads at a given locality are not each other’s closest relatives (are more distantly related, or non-monophyletic) and, thus, assembled ecologically, likely coexisting now as a result of their ecological tendencies toward distinct microhabitats (warmer stagnant pools in open areas, versus cool, flowing streams enclosed in forest). If these pairs of species types are determined to be the geographic norm among the more isolated, central, and northern, Philippine faunas, an obvious question will be whether they have evolved into dual ecological forms, possibly in response to ecological opportunity and/or reduced competition.« less
5. Short-distance gene flow and morphological divergence in Eschscholzia parishii (Papaveraceae): implications for speciation in desert winter annuals

   https://doi.org/10.1093/botlinnean/boac010  

   Spalink, Daniel ; Karimi, Nisa ; Richards, Jeannine H ; Eifler, Evan ; Dinicola, Alexa ; Thein, Thomas ; Schomaker, Lisa ; Drew, Bryan T ; Mcculloh, Katherine A ; Givnish, Thomas J ( March 2022 , Botanical Journal of the Linnean Society)

   Abstract Winter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal.