A stellar Stenella

The species name for the Clymene dolphin, Stenella clymene, likely was inspired by the water nymph daughter of the Titan Oceanus, also named Clymene [1]. This dolphin species is also commonly known as the short-snouted spinner dolphin, not to be confused with the Eastern spinner dolphin whom they frequently school with. The Clymene dolphin is very "acrobatic", often spinning and jumping out of the Atlantic waters they call home [2].

Research done on mitochondrial and nuclear markers in Amaral et al. (2014) shows that the Clymene dolphin is likely the result of the natural species hybridization between two Stenella species, Stenella coerueloalba and Stenella longisrostris. In this paper, the authors note that the cranial features of the Clymene dolphin closely resemble those of S. coeruleoalba, but its external appearance and behavior are more similar to those of S. longirostris. Natural hybridization in mammals is believed to be rare event but also an opportunity to share beneficial mutations and increase genetic diversity.

There is still much to be learned about this species, including their reproductive habits and lifespan. Although not endangered, the Clymene dolphin is protected under the CITES Appendix II [3]. One of the main threats to this species is getting entangled in fishing gear and nets. Ocean noise made by industrial and military boats also disturbs the Clymene dolphin, which rely on sound and echolocation to hunt, communicate like many other marine mammals.

Clymene dolphins, photo by Keith Mullin [NOAA/SEFSC MMPA Permit 779-1633]

Today, we share the chromosome-length genome assembly for the Clymene dolphin, Stenella clymene. The genome was assembled following the $1K strategy described in (Dudchenko et al., 2018). See our Methods page for more details.

This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The Clymene dolphin (Stenella clymene) specimen used in this study (Field ID WAM 602; Storage ID NM15K707C) was collected from from Topsail Island, NC by Bill McLellan (UNCW). This specimen was provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program.

This is the 4th Stenella dolphin species we've released so far. Check out the chromosome-length contact map for Stenella clymene below, and compare data to that released with the blog post by Ben Neely to learn more about other species in this fascinating genus of dolphins and compare their genome alignments! See also de novo assembly of the mitochondrion for the species shared in the full data release folder.

Potoroos in truffle

The critically endangered Gilbert's potoroo or Ngilkat (Potorous gilbertii) is believed to be Australia's rarest mammal and the world’s rarest marsupial.

Gilbert's potoroo is a small kangaroo-like marsupial in the family Potoroidae. It was first recorded for science in 1840 by the collector John Gilbert (hence the name). The few known historical records of the potoroo are all from the southwestern coast of Southwest Australia in 1843, 1866, 1869, and 1875, and the uncertain date of 1890s to the west. The species was believed to be extinct for over 100 years before it was rediscovered in 1994 in Two Peoples Bay Nature Reserve.

Photo Description – Gilbert's Potoroo or Ngilkat (Potorous gilbertii) Photo Courtesy – Dick Walker and GPAG

As soon as the species was rediscovered, it was recognised that the population was extremely vulnerable as it occurred in very long unburnt vegetation (60+ years) with high fuel loads and given its restricted distribution could be lost in a single fire.

For the past 25 years the Department of Biodiversity, Conservation and Attractions (DBCA) has undertaken a range of recovery actions including attempts at captive breeding and various types of assisted reproduction to establish a sufficiently large population of captive animals to use to create insurance populations in case the Two Peoples Bay population was lost. Unfortunately, due to Gilbert’s potoroo’s extremely specialist diet (over 90% hypogeal fungi, e.g. truffles, which makes it one of the most fungi-dependent mammals in the world) and possibly other genetic and behavioural characteristics, neither captive breeding nor any other assisted reproduction techniques were successful.

In 2005, DBCA and the Gilbert’s potoroo Recovery Team decided to abandon attempts at captive breeding and to focus instead on creating insurance populations at locations outside Two Peoples Bay. Ten animals were introduced to Bald Island east of Two Peoples Bay between 2005 and 2007 and into a 380-ha fenced enclosure at Waychinicup from 2010. In 2015 the long-predicted fire at Two Peoples Bay, ignited by a severe lightning storm, destroyed over 95% of Gilbert’s potoroo habitat leaving only about 5 survivors. A third safe haven population on Middle Island was created in 2018 to provide additional security for the species.

Gilbert’s potoroo is listed as Critically Endangered under the IUCN Red List, the Australian EPBC Act (1999) and the Western Australian Biodiversity Conservation Act (2016). The current population is estimated at about 100-120 individuals: Two Peoples Bay (about 3-5 animals), Bald Island (est. 70 animals), the Waychinicup enclosure (25 known animals) and Middle Island (10 translocated animals).

The long-term goal of the recovery program for Gilbert’s potoroo is to improve its conservation status by increasing both the size of existing populations and the number of populations. In order to do this, it is critical to understand the distribution of genetic diversity across the four sub-populations (wild and translocated) to inform population management strategies (including genetic augmentation or assisted gene flow) aimed at maximizing the retention of genetic diversity at the species level.

Today, we share the chromosome-length genome assembly for the Gilbert's potoroo. The assembly was generated using a sample from 2009 provided by Dr Tony Friend from DBCA. This is a $1K genome assembly, with contig N50 of 46kb and scaffold N50 of 558Mb. See our Methods page for more detail on the procedure.

The interactive contact map of the Gilbert's potoroo's chromosomes is included below, alongside the whole-genome alignment to another closely related marsupial from our collection, the tammar wallaby. Despite the close chromosome count, the whole-genome alignment suggests substantial interchromosomal rearrangements since the last common ancestor of the two species (estimated to have existed ~24 MYA). This is the first version of the genome assembly for the species ever. Since our first tackle at this, we've generated more data and hope to generate even more, so stay tuned!

The work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Illumina Inc., Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. The work was provided as an in-kind contribution to a Western Australian State Natural Resource Management Community Stewardship Grant awarded to the Gilbert's Potoroo Action Group, a volunteer community group seeking to help save Gilbert's potoroo.

Whole-genome alignment plot between the Gilbert's potoroo chromosome-length genome assembly (Potorous_gilbertii_HiC, 2n=12,13) and a closely related marsupial from our collection, the tammar wallaby (me-1k, 2n=16). Both genome assemblies are $1K genome assemblies.

We hope that this chromosome-length assembly will provide the genomics resource to assist in estimating the genome-wide genetic diversity present in the existing population as well as management of the species. We also hope that this data will enable research on genes involved in adaptation and disease, further increasing our ability to improve species resilience in the population management strategy. Working with the Gilbert's potoroo recovery team this resource will facilitate the integration of genetic information into conservation management for the species. We believe that creation of this genomic resource will have lasting benefits for the genetic management and long-term survival of this critically endangered species.

Join Gilbert’s Potoroo Action Group (GPAG), DNA Zoo Australia/University of Western Australia & Department of Biodiversity, Conservation & Attractions for an afternoon event Saturday September 4, 2021, 1:00pm - 4:00pm to unveil the genome puzzle for the world's rarest marsupial, Gilbert’s Potoroo, & learn about the importance of genetics for endangered species conservation. The genome will be launched by former WA Chief Scientist Prof Lyn Beazley & followed by a truffle-themed afternoon tea & time for discussion, socialising & participation in puzzles & activities.

Free event book here https://www.trybooking.com/events/landing?eid=798292&

Ba-da-bing, ba-da baboon

The Guinea baboon, Papio papio, is one of the smallest of all baboon species. While male Guinea baboons are larger than their female counterparts, they still typically reach a maximum height just under 3 feet tall [1]. They're covered in reddish brown fur with the exception of their faces and their rumps which are bright pink. Only male Guinea baboons possess the impressive large canines, another instance of sexual dimorphism in this species [2].

Like many primate species, Guinea baboons have complex social structures and can live in large communities, sometimes as many as 200 individuals [3]! Most often, Guinea baboons live in one male unit (OMUs) with a harem of female baboons to mate with. Sexually mature male baboons leave their familial groups to form All Male Units (AMUs). Different OMUs may congregate to form larger groups depending on resources or other environmental circumstances [4].

Baboon by Cloudtail the Snow leopard, [CC BY-NC-ND 2.0], via flickr.com

Today, we share the chromosome-length genome assembly for the Guinea baboon, Papio papio. This genome assembly was generated using data from a primary fibroblast cell line from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center, originally frozen in 1978. Check out our Methods page for assembly procedure details and stay tuned, as always, for more chromosome-length genome assemblies from the T.C. Hsu Cryo-Zoo collection!

Check out below how the chromosomes in the guinea baboon relate to those of humans (~29MY to common ancestor, per timtree.org), and explore the interactive contact map of the chromosomes. Find out more on the corresponding assembly page!

Whole-genome alignment plot between the new chromosome-length assembly for the guinea baboon (Papio_papio_HiC, 2n=42) and the human genome assembly (GRCh38, 2n=46).

Correction: the original version of the blog post stated that the Guinea baboon was the smallest of all baboons. It is in fact one of the smallest, with Kinda baboons having smaller average body mass [5].