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1. 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 themore »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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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. 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)

   To 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.

   Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia.

   Order Rodentia, Family Muridae.

   We 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.

   We 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.

   Our 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 occurringmore »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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4. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia , an Australian endemic genus of Cycadales

   https://doi.org/10.1093/aob/mcac117  

   Habib, Sadaf ; Gong, Yiqing ; Dong, Shanshan ; Lindstrom, Anders ; William Stevenson, Dennis ; Liu, Yang ; Wu, Hong ; Zhang, Shouzhou ( September 2022 , Annals of Botany)

   Abstract Background and Aims Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. Methods We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. Key Results The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamiamore »is estimated to around 11.80 Ma, with a major expansion in the last 5–6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. Conclusions This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.« less
5. Montane regions shape patterns of diversification in small mammals and reptiles from Madagascar’s moist evergreen forest

   https://doi.org/10.1111/jbi.13945  

   Everson, Kathryn M. ; Jansa, Sharon A. ; Goodman, Steven M. ; Olson, Link E. ( September 2020 , Journal of Biogeography)

   Madagascar is renowned for its exceptional species diversity and endemism. The island's mountainous regions are thought to have played a role in lineage and species diversification, but this has yet to be explored across taxonomic groups and a temporal context has not yet been identified. We tested whether montane regions have promoted population divergence in Madagascar's vertebrate fauna and, if so, whether these divergence events were contemporaneous.

   Moist evergreen forests of Madagascar.

   Small mammals and reptiles.

   We analysed mitochondrial DNA data from 20 small‐mammal and five reptile species widely distributed across Madagascar's moist evergreen forests. We used phylogenetic and population genetic analyses to identify major phylogeographic patterns, then used linear regression to determine if the strength of phylogeographic structure is related to taxon, body size or elevation. Finally, we tested whether or not divergence across highlands occurred synchronously in multiple species, and used simulations to assess the power of these analyses to accurately estimate divergence times.

   We observed a shared phylogeographic pattern across multiple species that suggests Madagascar's northern, central and southern highlands have served as important regions of diversification on Madagascar. This pattern was recovered across taxa with varying body sizes and elevational distributions. We also identified fourmore »pulses of divergence between the northern and central highlands since the late Miocene, although simulations suggest that our empirical data cannot recover the number or timing of divergence events with high certainty. Finally, we observed several instances of deep intraspecific genetic splits, suggesting that several of the species we evaluated may represent cryptic species complexes.

   We identified a highland‐driven phylogeographic pattern plus several cases of cryptic endemism and recent speciation, which have important evolutionary and conservation implications. This work presents a new phylogeographic hypothesis for recent diversification on Madagascar, reaffirms the urgent need for continued collection of voucher specimens and illuminates areas of particular importance for safeguarding genetic diversity in one of the world's foremost and threatened biodiversity hotspots.

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