Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H. 2021. doi:http://dx.doi.org/10.14288/1.0397698

Abstract

The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence.

A survey of small mammals in the Volta Region of Ghana with comments on zoogeography and conservation

Jan DECHER, Ryan W. NORRIS, Michael ABEDI-LARTEY, James OPPONG, Rainer HUTTERER, Martin WEINBRENNER, Martin KOCH, Lars PODSIADLOWSKI & C. William KILPATRICK. 2021 ZOOSYSTEMA 43 (14) - PAGES 253-281. https://doi.org/10.5252/zoosystema2021v43a14

Abstract

We examined small mammal (insectivores, bats and rodents) diversity in community and legally protected forest remnants in the Ghana-Togo Highlands of the Volta Region of Ghana, West Af-rica, a zoologically understudied area compared to neighboring Togo to the East, or Ghana west of the Volta River. We recorded 34 small mammal species: three species of shrews (Soricidae Fischer, 1815), 12 species of rodents, one primate (Galagidae Gray, 1825) and 17 species of bats (Chiroptera Blumenbach, 1779). The rodent Stochomys longicaudatus (Tullberg, 1893) appears to be a first record for Ghana. Two shrew, three rodent and one bat species were first records for the Volta Region. By comparing our small mammal captures and limited microhabitat data from 1999 and 2001 to forest cover change maps for the period 2000-2015 we discuss trends in species community changes due to forest cover loss and other disturbance regimes. Aside from contributing to our understanding of the distribution of several small mammal species, the study demonstrates the progressive loss of forest habitat in the Volta Region

A re-examination of the molecular systematics and phylogeography of taxa of the Peromyscus aztecus species group, with comments on the distribution of P. winkelmanni

C. William Kilpatrick, Nelish Pradhan, and Ryan W. Norris. THERYA, 2021, Vol. 12(2):331-346. DOI:10.12933/therya-21-1115.

Abstract

The objectives of this study are to examine the available molecular data from the mitochondrial cytochrome-b gene (Cytb) and a concatenated dataset with this gene and two nuclear introns (Adh-1-I2 and Fgb-I7) to reexamine the systematic and phylogeographic conclusions reached by Sullivan et al. (1997) concerning the Peromyscus aztecus species group. The divergence of samples of P. aztecus oaxacensis across the Isthmus of Tehuantepec are further examined and taxonomic revisions are suggested. In addition, this study reviews the sources of data that lead to the conclusion that P. winkelmanni occurred in the Sierra Madre del Sur in Guerrero including a morphometric examination of a reported voucher. Bayesian and maximum likelihood analyses were conducted on a dataset of 31 Cytb sequences of all taxa in the P. aztecus group except for P. a. cordillerae and a concatenated dataset including five individuals of this group. Representative taxa of the P. boylii, P. mexicanus, and P. truei groups were included in both analyses. Body and cranial measurements of the voucher of the P. winkelmanni from Guerrero from which a Cytb sequence is reported to have been obtained was compared with measurements from specimens taken from the vicinity of Dos Aguas, Michoacán, including the type locality. We identified seven instances involving problematic identifications in GenBank. Once these issues were addressed, well-supported monophyletic sister clades of the P. aztecus and P. boylii species groups were recovered from phylogenetic analyses of Cytb sequences (Fig 1). Phylogenetic analyses of the Cytb and the concatenated datasets recover similar topologies that support the relationships of taxa of the aztecus group proposed by an earlier molecular study. Populations of P. a. oaxacensis southeast of the Isthmus of Tehuantepec represent a distinct species. Measurements of the voucher from Guerrero identified as the source of a P. winkelmanni Cytb sequence are smaller than P. winkelmanni for several characters. The divergent populations of P. a. oaxacensis from southeast of the Isthmus of Tehuantepec are recognized as two subspecies of P. cordillerae, P. c. cordillerae and P. c. hondurensis, whereas those northwest of the Isthmus are retained as P. a. oaxacensis. The lack of genetic divergence observed between P. a. evides and P. a. oaxacensis questions whether these two taxa should continue to be recognized as separate subspecies. Northern and southern populations of P. spicilegus demonstrate moderate divergence and additional examination of morphological and molecular differentiation within this taxon is warranted. The distribution of P. winkelmanni should be restricted to the vicinity of Dos Aguas, Michoacán, due to the lack of a voucher specimen that would confirm its reported occurrence in Guerrero.

Cross-tolerance and transcriptional shifts underlying abiotic stress in the seabird tick, Ixodes uriae

Benjamin Davies, Andrew J. Rosendale, Josiah D. Gantz, Richard E. Lee Jr., David L. Denlinger & Joshua B. Benoit 
Polar Biology volume 44, pages1379–1389 (2021). https://doi.org/10.1007/s00300-021-02887-4

Abstract

The seabird tick, Ixodes uriae, is a significant ectoparasite of penguins in Antarctica and of other seabirds, mainly in coastal, polar regions of the Northern and Southern hemispheres, but the tick’s distribution extends into more temperate regions as well. The expansive range of this tick suggests that it is exposed to a wide range of abiotic stresses, including dehydration, heat, and cold. To better understand how I. uriae responds to stress exposure, we examined cross-tolerance between dehydration and thermal stress based on survival analyses and used RNA-seq to monitor transcriptional responses to cold, heat, and dehydration. Slight dehydration improved cold, but not heat tolerance, whereas severe dehydration reduced subsequent thermal tolerance. Dehydration exposure prompted transcript-level shifts underlying protein metabolism, recovery from stress, and processes allowing subsequent rehydration by water vapor uptake. Both cold and heat stress yielded expression changes involved in cuticle modification. One gene increased in expression (enzyme P450) and one decreased (transcription factor Hairy) in response to all three stresses. This study provides the groundwork for assessing stress tolerance in this bipolar ectoparasite.

Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans

Heather Glon, Andrea Quattrini, Estefanía Rodríguez, Benjamin M.Titus, Marymegan Daly. Molecular Phylogenetics and Evolution. Volume 163, October 2021. https://doi.org/10.1016/j.ympev.2021.107233

Abstract

Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.