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1. Oceanic islands of Wallacea as a source for dispersal and diversification of murine rodents

   https://doi.org/10.1111/jbi.13720  

   Rowe, Kevin_C; Achmadi, Anang_S; Fabre, Pierre‐Henri; Schenk, John_J; Steppan, Scott_J; Esselstyn, Jacob_A (October 2019, Journal of Biogeography)

   Abstract AimTo determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. LocationIndo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. TaxonOrder Rodentia, Family Muridae. MethodsWe used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. ResultsWe identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genusRattusand their closest relatives, irrespective of colonization history. Main ConclusionsOur inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations. 

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2. Has past climate change affected cold‐specialized species differentially through space and time?

   https://doi.org/10.1111/syen.12341  

   Schoville, Sean D.; Bougie, Tierney C.; Dudko, Roman Y.; Medeiros, Matthew J. (December 2018, Systematic Entomology)

   Abstract Quaternary climate change has been strongly linked to distributional shifts and recent species diversification. Montane species, in particular, have experienced enhanced isolation and rapid genetic divergence during glacial fluctuations, and these processes have resulted in a disproportionate number of neo‐endemic species forming in high‐elevation habitats. In temperate montane environments, a general model of alpine population history is well supported, where cold‐specialized species track favourable climate conditions downslope during glacial episodes and upslope during warmer interglacial periods, which leads to a climate‐driven population or species diversification pump. However, it remains unclear how geography mediates distributional changes and whether certain episodes of glacial history have differentially impacted rates of diversification. We address these questions by examining phylogenomic data in a North American clade of flightless, cold‐specialized insects, the ice crawlers (Insecta: Grylloblattodea: Grylloblattidae:Grylloblatta). These low‐vagility organisms have the potential to reveal highly localized refugia and patterns of spatial recolonization, as well as a longer history of in situ diversification. Using continuous phylogeographic analysis of species groups, we show that all species tend to retreat to nearby low‐elevation habitats across western North America during episodes of glaciation, but species at high latitude exhibit larger distributional shifts. Lineage diversification was examined over the course of the Neogene and Quaternary periods, with statistical analysis supporting a direct association between climate variation and diversification rate. Major increases in lineage diversification appear to be correlated with warm and dry periods, rather than with extreme glacial events. Finally, we identify substantial cryptic diversity among ice crawlers, leading to high endemism across their range. This diversity provides new insights into highly localized glacial refugia for cold‐specialized species across western North America. 

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3. Diversification and post-glacial range expansion of giant North American camel spiders in genus Eremocosta (Solifugae: Eremobatidae)

   https://doi.org/10.1038/s41598-021-01555-1  

   Santibáñez-López, Carlos E.; Cushing, Paula E.; Powell, Alexsis M.; Graham, Matthew R. (December 2021, Scientific Reports)

   Abstract Species of camel spiders in the family Eremobatidae are an important component of arthropod communities in arid ecosystems throughout North America. Recently, research demonstrated that the evolutionary history and biogeography of the family are poorly understood. Herein we explore the biogeographic history of this group of arachnids using genome-wide single nucleotide polymorphism (SNP) data, morphology, and distribution modelling to study the eremobatid genus Eremocosta , which contains exceptionally large species distributed throughout North American deserts. Relationships among sampled species were resolved with strong support and they appear to have diversified within distinct desert regions along an east-to-west progression beginning in the Chihuahuan Desert. The unexpected phylogenetic position of some samples suggests that the genus may contain additional, morphologically cryptic species. Geometric morphometric analyses reveal a largely conserved cheliceral morphology among Eremocosta spp. Phylogeographic analyses indicate that the distribution of E. titania was substantially reduced during the last glacial maximum and the species only recently colonized much of the Mojave Desert. Results from this study underscore the power of genome-wide data for unlocking the genetic potential of museum specimens, which is especially promising for organisms like camel spiders that are notoriously difficult to collect. 

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

   https://doi.org/10.1093/sysbio/syab034  

   Chan, Kin Onn; Hutter, Carl R; Wood, Perry L; Su, Yong-Chao; Brown, Rafe M (May 2021, Systematic Biology)

   Burbrink, Frank (Ed.)

   Abstract 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 specific ways in which gene flow can 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. We 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-by-distance, 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. [Cryptic species; gene flow; introgression; isolation-by-distance; isolation-by-environment; phylogenetic network; species delimitation.] 

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5. 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)

   null (Ed.)

   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. We 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. 

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