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1. Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

   https://doi.org/10.1111/jbi.13748  

   Marques-Souza, Sergio ; Machado_Pellegrino, Katia_C ; Oliveira_Brunes, Tuliana ; Carnaval, Ana_Carolina ; Pacheco_Damasceno, Roberta ; Lima_de_Oliveira_Borges, Manoela ; Candia_Gallardo, Carlos ; Rodrigues, Miguel_Trefaut ( December 2019 , Journal of Biogeography)

   To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.

   Central Amazonia, Brazil.

   Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

   We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).

   We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

   Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

    

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2. Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA ‐seq analyses

   https://doi.org/10.1002/ece3.1865  

   Edwards, Taylor ; Tollis, Marc ; Hsieh, PingHsun ; Gutenkunst, Ryan N. ; Liu, Zhen ; Kusumi, Kenro ; Culver, Melanie ; Murphy, Robert W. ( January 2016 , Ecology and Evolution)

   Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genusGopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNAand four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree.RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).

    

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3. Phylogeography, Historical Population Demography, and Climatic Modeling of Two Bird Species Uncover Past Connections Between Amazonia and the Atlantic Forest

   https://doi.org/10.1002/ece3.70587  

   Castro‐Astor, Ivandy_N ; Cracraft, Joel ; Tello, José_G ; Alves, Maria_Alice_S ; Mauck, III, William_M ; Aleixo, Alexandre ; Duca, Charles ; Carnaval, Ana_Carolina ( December 2024 , Ecology and Evolution)

   We combined mitochondrial DNA sequence data and paleoclimatic distribution models to document phylogeographic patterns and investigate the historical demography of two manakins,Ceratopipra rubrocapillaandPseudopipra pipra, as well as to explore connections between Amazonia and the Atlantic Forest. ND2 sequences ofC. rubrocapilla(75 individuals, 24 sites) andP. pipra(196, 77) were used in Bayesian inference and maximum likelihood analyses. We estimated mitochondrial nucleotide diversity, employed statistical tests to detect deviations from neutral evolution and constant population sizes, and used species distribution modeling to infer the location of suitable climate for both species under present‐day conditions, the Last Glacial Maximum (LGM), and the Last Interglacial Maximum (LIG). Mitochondrial sequence data fromC. rubrocapillaindicate one Amazonian and one Atlantic Forest haplogroup. InP. pipra, we recovered a highly supported and differentiated Atlantic Forest haplogroup embedded within a large Southern Amazonian clade. Genetic and taxonomic structure in Amazonia differs widely between these two species; olderP. piprahas a more marked genetic structure and taxonomic differentiation relative to the youngerC. rubrocapilla. Both species have similar genetic patterns in the Atlantic Forest. Paleoclimatic distribution models suggest connections between southwestern Amazonia and the southern Atlantic Forest during the LIG, but not between eastern Amazonia and the northeastern Atlantic Forest, as suggested by previous studies. This indicates that multiple corridors, and at different locations, may have been available over the Pliocene and Pleistocene between these two regions.

    

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4. Bayesian analyses detect a history of both vicariance and geodispersal in Neotropical freshwater fishes

   https://doi.org/10.1111/jbi.13207  

   Machado, Carolina Barros ; Galetti, Jr, Pedro Manoel ; Carnaval, Ana Carolina ( March 2018 , Journal of Biogeography)

   Among the main biogeographical hypotheses explaining the remarkable diversity of fishes in the Neotropics is the “palaeogeographical hypothesis”, focusing on vicariance, and the “hydrogeological hypothesis”, focusing on geodispersal. Yet while reflecting different processes, they may result in similar biogeographical patterns. We employed a model‐based Bayesian approach to test these alternative hypotheses and determine which shaped the phylogeographical patterns observed in a group of Neotropical fishes.

   South America.

   Salminus.

   We used mitochondrial and nuclear markers to infer phylogenetic relationships and estimate divergence times amongSalminusspecies, associating the results with known geological events. We then employed approximate Bayesian computation (ABC) to explore changes in population size over time, asking whether vicariance or geodispersal events best explain the phylogeographical signature observed in the data. Because geodispersal captures a few individuals from a parental population, which can then expand and lead to a new lineage, we expect to find genetic signatures of a founder event following population expansion under this scenario, but not under vicariance.

   The analyses suggest that the diversification process inSalminusbegan in Upper Miocene, andABCindicates that it involved both vicariance and geodispersal events: while a vicariance event better explains the phylogeographical structure withinS. brasiliensisand the genetic patterns of differentiation betweenS. sp. Amazon andS. sp. Araguaia, geodispersal appears to have been the most important event structuring lineages ofSalminus hilarii.

   Both vicariance and geodispersal signatures were detected in our biological model, inferring a complex yet realistic demographic history ofSalminuslineages. The correspondence between theABCresults and traditional phylogeographical interpretations provide further confidence in the models drawn and tested. This study reinforces the value of applying anABCframework in phylogeographical studies, particularly for those interested in testing alternative and biologically plausible processes underlying similar biogeographical patterns.

    

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5. Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo‐West Pacific

   https://doi.org/10.1111/jbi.13231  

   Titus, Benjamin M. ; Daly, Marymegan ; Hamilton, Natalie ; Berumen, Michael L. ; Baeza, J. Antonio ( April 2018 , Journal of Biogeography)

   The “sexy shrimp”Thor amboinensisis currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis thatT. amboinensisis a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic.

   Coral reefs in all tropical oceans.

   Specimens ofThor amboinensiswere obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals, 30 sample localities), while phylogeographical reconstruction in theTWAwas based onCOIonly (n = 303 individuals, 10 sample localities).

   We found evidence for at least five cryptic lineages (9%–22%COIpairwise sequence divergence): four in the Indo‐West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co‐occurring lineage that is widespread throughout the Indo‐West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km.

   Thor amboinensisis a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo‐West Pacific. Nuclear‐ and mitochondrial‐ gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between multi‐locus analyses suggest thatT. amboinensisoriginated in the Tethys sea and dispersed into the Atlantic and Indo‐West Pacific through the Tethys seaway or, alternatively, originated in the Indo‐West Pacific and dispersed into the Atlantic around South Africa. Population‐level patterns in the Caribbean indicate extensive gene flow across the region.

    

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