Evolving in isolation: Genetic tests reject recent connections of Amazonian savannas with the central Cerrado

AimThe effects of past climatic shifts remain enigmatic for the Amazon region, especially for islands of savanna within the tropical forest known as â Amazonian savannasâ (AS). These disjunct savanna areas share many plant and animal species with the Cerrado biome in central Brazil (the CC), fuelling debate over historical connections. We evaluate hypothesized corridors between the CC and the AS, and specifically investigate whether a history of isolation versus recent connections is supported by genetic tests.LocationCerrado and Amazon biomes.TaxonTwo woody plant species: Byrsonima coccolobifolia and B. crassifolia (Malpighiaceae).MethodsAnalyses of genomic data (SNPs from more than 4,500 loci) in 28 populations, as well as chloroplast DNA (cpDNA), were used to test for parallel geographic structuring between the CC and ASâ an expected structure if putative corridors provided regional connections between different areas of the CC and AS, and divergence times between the CC and AS were estimated using a compositeâ likelihood method based on the site frequency spectrum.ResultsGenomic data, in contrast with cpDNA, generally show strong, concordant genetic structure between the CC and AS in both species, rather than regional grouping of CC with AS populations. In addition, divergence between the CC and AS predates the Last Glacial Maximum.Main conclusionsOur results suggest the AS have remained relatively isolated from the CC even though the strong structure of genomic variation is not shared by cpDNA. We note that past evidence of putative corridors between the CC and AS based solely on cpDNA should be interpreted cautiously since the lack of structure may reflect limited genetic resolution rather than gene flow. As such, the uniqueness of AS may be more pronounced than previously thought, highlighting the importance of protecting these highly threatened areas.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147774/1/jbi13468_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147774/2/jbi13468.pd

High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered

Beyond Refugia: New insights on Quaternary climate variation and the evolution of biotic diversity in tropical South America

Haffer’s (Science 165: 131–137, 1969) Pleistocene refuge theory has provided motivation for 50 years of investigation into the connections between climate, biome dynamics, and neotropical speciation, although aspects of the orig- inal theory are not supported by subsequent studies. Recent advances in paleocli- matology suggest the need for reevaluating the role of Quaternary climate on evolutionary history in tropical South America. In addition to the many repeated large-amplitude climate changes associated with Pleistocene glacial-interglacial stages (~40 kyr and 100 kyr cyclicity), we highlight two aspects of Quaternary climate change in tropical South America: (1) an east-west precipitation dipole, induced by solar radiation changes associated with Earth’s precessional variations (~20 kyr cyclicity); and (2) periods of anomalously high precipitation that persisted for centuries-to-millennia (return frequencies ~1500 years) congruent with cold “Heinrich events” and cold Dansgaard-Oeschger “stadials” of the North Atlantic region. The spatial footprint of precipitation increase due to this North Atlantic forcing extended across almost all of tropical South America south of the equator. Combined, these three climate modes present a picture of climate change with different spatial and temporal patterns than envisioned in the original Pleistocene refuge theory. Responding to these climate changes, biomes expanded and contracted and became respectively connected and disjunct. Biome change undoubtedly influenced biotic diversification, but the nature of diversification likely was more complex than envisioned by the original Pleistocene refuge theory. In the lowlands, intermittent forest expansion and contraction led to species dispersal and subsequent isolation, promoting lineage diversification. These pulses of climate-driven biotic interchange profoundly altered the composition of regional species pools and triggered new evolutionary radiations. In the special case of the tropical Andean forests adjacent to the Amazon lowlands, new phylogenetic data provide abundant evidence for rapid biotic diversification during the Pleistocene. During warm interglacials and intersta- dials, lowland taxa dispersed upslope. Isolation in these disjunct climate refugia led to extinction for some taxa and speciation for others.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155561/1/Baker2020.pdfDescription of Baker2020.pdf : Main articl

The herpetofauna of Sonora, Mexico, with comparisons to adjoining states

Situated in the topographically complex transition between the Neotropics and the temperate biomes of North America, the state of Sonora, Mexico, has an extraordinarily diverse herpetofauna. Surprisingly little research has been conducted on the state’s amphibians and reptiles and many systematic and biogeographic questions remain unanswered. To facilitate future research, we provide a checklist of Sonora’s herpetofauna, documenting species presence based on museum specimens, our fieldwork, and published research. Sonora’s herpetofauna is placed in a regional biogeographic perspective via a checklist for the six adjoining states together with faunal analyses. A total of 402 species of amphibians and reptiles are recorded from these seven states. Sonora has the greatest species richness (187 species), followed by Chihuahua (169 species), and Sinaloa (146 species). Sonora's herpetofauna is most similar to that of Chihuahua, with which it shares a long border. Eleven biogeographic affinity-based faunal groups are recognized. Of these, three are dominant in Sonora: a core group classified as "Sonoran" demonstrates strong affinity to Sonoran Desertscrub and Sinaloan Thornscrub communities; a Tropical group - with many species reaching their northern distributional limits in the state; and a Madrean group consisting largely of montane species. Our state-level faunal analysis provides some evidence of peninsular depauperization of the herpetofauna on the Baja California peninsula due in part to the small number of Neotropical species present in Baja California Sur. Our faunal analysis points toward distinctive mainland and peninsular Sonoran Desert herpetofaunas centered on Sonora and the Baja California Peninsula, respectively, each with about 50 non-insular species, and each with species-level endemism nearing 50%.

The herpetofauna of Sonora, Mexico, with comparisons to adjoining states

Situated in the topographically complex transition between the Neotropics and the temperate biomes of North America, the state of Sonora, Mexico, has an extraordinarily diverse herpetofauna. Surprisingly little research has been conducted on the state’s amphibians and reptiles and many systematic and biogeographic questions remain unanswered. To facilitate future research, we provide a checklist of Sonora’s herpetofauna, documenting species presence based on museum specimens, our fieldwork, and published research. Sonora’s herpetofauna is placed in a regional biogeographic perspective via a checklist for the six adjoining states together with faunal analyses. A total of 402 species of amphibians and reptiles are recorded from these seven states. Sonora has the greatest species richness (187 species), followed by Chihuahua (169 species), and Sinaloa (146 species). Sonora's herpetofauna is most similar to that of Chihuahua, with which it shares a long border. Eleven biogeographic affinity-based faunal groups are recognized. Of these, three are dominant in Sonora: a core group classified as "Sonoran" demonstrates strong affinity to Sonoran Desertscrub and Sinaloan Thornscrub communities; a Tropical group - with many species reaching their northern distributional limits in the state; and a Madrean group consisting largely of montane species. Our state-level faunal analysis provides some evidence of peninsular depauperization of the herpetofauna on the Baja California peninsula due in part to the small number of Neotropical species present in Baja California Sur. Our faunal analysis points toward distinctive mainland and peninsular Sonoran Desert herpetofaunas centered on Sonora and the Baja California Peninsula, respectively, each with about 50 non-insular species, and each with species-level endemism nearing 50%.