Methods

Tissues for this study were collected from wild-caught individuals in the Ecuadorian provinces of Pichincha and Manabí. Samples were collected in 2021 and 2022 by AL and JRD under permit MAE-DNB-CM-2018-0105 issued to Universidad San Francisco de Quito by the Ecuadorian Ministry of the Environment. Tissues were deposited at the Universidad San Francisco de Quito and subsequently loaned to the Field Museum of Natural History.

DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v2.5 (Bankevich et al. 2012) followed by a finishing step using Zanfona (M., K., and S. 2021).

Results and Data Availability

All genome sequences are available on Genbank:

 
Acropternis orthonyx IRGN AL808 JAWWEU000000000
Anabacerthia variegaticeps IRGN AL189 JAWWEW000000000
Anisognathus igniventris IRGN AL800 JAWWET000000000
Arremon aurantiirostris IRGN AL570 JAXCLO000000000
Arremon brunneinucha IRGN AL096 JAWWEX000000000
Basileuterus tristriatus IRGN AL131 JAWWMR000000000
Catamblyrhynchus diadema IRGN AL882 JAWWMN000000000
Chlorospingus flavigularis IRGN AL118 JAWWMQ000000000
Chlorospingus semifuscus IRGN AL824 JAWWMS000000000
Cinnycerthia olivascens IRGN AL742 JAWWMU000000000
Cinnycerthia unirufa IRGN AL889 JAWWMV000000000
Dendrocincla fuliginosa IRGN AL075 JAWWMO000000000
Dendrocincla tyrannina IRGN AL879 JAWWMP000000000
Diglossa cyanea IRGN AL854 JAWWMT000000000
Euphonia xanthogaster IRGN AL161 JAYDZK000000000
Gymnopithys bicolor IRGN AL540 JAWWLY000000000
Hafferia zeledoni IRGN AL102 JAWWEV000000000
Lepidocolaptes lacrymiger IRGN AL467 JAXCLP000000000
Lophotriccus pileatus IRGN AL172 JAWWES000000000
Margarornis squamiger IRGN AL498 JAWWTY000000000
Mionectes olivaceus IRGN AL036 JAWWMA000000000
Myioborus melanocephalus IRGN AL886 JAWWLS000000000
Myioborus miniatus IRGN AL290 JAWWEB000000000
Myiothlypis chrysogaster IRGN AL104 JAWWLX000000000
Myiothlypis coronata IRGN AL392 JAWWLW000000000
Myiotriccus ornatus IRGN AL167 JAYRBT000000000
Platyrinchus mystaceus IRGN AL083 JAWWLV000000000
Poliocrania exsul IRGN AL078 JAWWLZ000000000
Premnoplex brunnescens IRGN AL133 JAWWLT000000000
Pseudotriccus pelzelni IRGN AL266 JAWMRA000000000
Sphenopsis melanotis IRGN AL450 JAWMRF000000000
Syndactyla subalaris IRGN AL174 JAWMRD000000000
Tachyphonus luctuosus IRGN AL191 JAWWEY000000000
Tangara arthus IRGN AL149 JAWMQZ000000000
Thripadectes ignobilis IRGN AL114 JAWMRC000000000
Xenops minutus IRGN AL101 JAWWEE000000000
Xiphorhynchus erythropygius IRGN AL109 JAWMRB000000000

Funding

Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.